Table 1.
List of prokaryotic representative species in Fig 1.
Table 2.
11 viral sequences consisting of Ku70/80 beta-barrel domain.
Table 3.
List of 61 representative eukaryotes in which the presence of Ku70/80 was searched in OrthodB.
Table 4.
The number of different groups of organisms included in Fig 1.
Fig 1.
A representative Ku phylogenetic tree of 100 Ku70, Ku80, viral, and prokaryotic Ku sequences.
The tree was drawn using the Maximum Likelihood method in PhyML. Automatic model selection based on the lowest BIC (Bayesian Information Criterion) was done using Smart Model Selection (SMS). Support for each branch was established using Shimodaira–Hasegawa [SH]-aLRT (approximate Likelihood Ratio Test). Mid-point rooting was performed using Mega11. Unsupported nodes ([SH]-aLRT < 50%) are excluded.
Fig 2.
Collapsed phylogenetic trees of (a) 1097 Ku70 orthoDB sequences and (b) 1256 Ku80 OrthoDB sequences.
Trees were drawn using the Maximum Likelihood method in PhyML. Automatic model selection based on the lowest BIC (Bayesian Information Criterion) was done using Smart Model Selection (SMS). Support for each branch was established using Shimodaira–Hasegawa [SH]-aLRT (approximate Likelihood Ratio Test). Trees have been simplified for better visualization using Figtree. Monophyletic clades are collapsed into triangles. The clades that harbored species spanning multiple groups were annotated based on the dominant group. The area of the triangle is not proportional to the number of Ku sequences. The trees were rooted using M. tuberculosis as the outgroup.
Fig 3.
VWA, KU70/80 beta-barrel domain, Ku C terminal, and other Ku70 domains of representative species determined using InterPro.
(a) Animalia (b) Choanoflagellate (c) Fungi. (d) Ichthyosporea (e) Chloroplastida (f) Alveolata (g) Amoebozoa (h) Discoba.
Fig 4.
VWA, KU70/80 beta-barrel domain, Ku C terminal, and other Ku80 domains of representative species determined using InterPro.
(a) Animalia (b) Choanoflagellate (c) Fungi. (d) Ichthyosporea (e) Chloroplastida (f) Alveolata (g) Amoebozoa (h) Discoba.
Fig 5.
A model of inheritance of Ku across domains [21].
The figure above describes the phylogenetic classification of the domain eukarya into groups [23,31]. The earliest eukaryotes possibly inherited primitive Ku protein. Gene duplication might have occurred in some ancestral Excavate, leading to the formation of Ku70 and Ku80. These Ku proteins were then vertically inherited by eukaryotic groups: Discoba, Opisthokonta, Amoebozoa, TSAR, and Archaeplastida.
Fig 6.
Structural Overlay of Experimental Human Ku Core Protein Against Protein Subsets from Various Species.
(a-h) Overlay of the human Ku70 core (magenta) with the Ku70 core from Mycobacterium phage Thibault, Mycobacterium tuberculosis, Methanocella paludicola SANAE, Trypanosoma cruzi KU70, Saccharomyces cerevisiae KU80, Arabidopsis thaliana Ku70, Homo sapiens Ku70, and Homo sapiens Ku80. (i-q) Overlay of the human Ku80 core (grey) with the Ku80 core from Trypanosoma brucei KU80, Saccharomyces cerevisiae KU80, Mycobacterium phage Thibault, Mycobacterium tuberculosis, Tetrahymena thermophila transposon, Methanocella paludicola SANAE, Homo sapiens Ku70, Arabidopsis thaliana Ku80, and Homo sapiens Ku80.