(A) Under aerobic conditions, electrons from NADH or succinate (Suc) are shuttled to ubiquinone (UQ) via Complex I (I) or Complex II (II) respectively to generate NAD (NAD+), fumarate (fum) and …
Eukaryotic proteins are coloured based on their phylogenetic affiliations: Obazoa (purple), Stramenopiles-Alveolata (orange), Excavata (green), Amoebozoa (magenta) and Rhizaria (blue). Hexagons …
Nucleotide from both transcriptome and genomic sequencing projects (when available) were aligned using Sequencher (Gene Codes v 5.4.6) and introns were manually inspected for position, length and …
Maximum likelihood analysis of a 200 phylum-specific phylogenetic marker genes representing 54,400 sites from 210 representative alphaproteobacteria under the LG + C60 + F (PMSF)+ Γ4 model of …
Conserved residues known to interact with the carbonyl group of SAM are shown with black triangles. A substitution from aspartate to glutamine was obversed in all bacterial (represented here by Rhodo…
Eukaryotic genomes and transcriptomes were surveyed for homologs of respiratory chain components (Complexes I-V, CI-CV), alternative oxidase (AOX), dihydroorotate dehydrogenase (DHOH), …
(A) Antibodies raised against RquA (green) colocalized with MitoTracker (red). Confocal slices (0.3 μm) were deconvoluted (using a constrained interative algorithm) and combined to render a 3D …
Proteins isolated from whole cell extracts of E. coli induced to express pGEX4T-1 (1) and pGEX- Pb-rquA (2) and glutathione-S-transferase(GST)-Pb-rquA purified with glutathione magnetic beads (3) …
Spectra represent the elution times of detection of the rhodoquinone head group (182.1 m/z; left) and ubiquinone head group (197.1 m/z) following fragmentation of parent ions of different isoprenyl …
Standard reduction potentials for each major reaction involved in rhodoquinone (R)) and ubiquinone (U) metabolism are shown in increasing order of potential. Half reaction equations are detailed in s…
Monophyly Tested | Tree file | CONSEL p-AUa |
---|---|---|
Group A and Group B | ||
Maximum likelihood tree | Figure 2; Supplementary file 2 - tree 2 | 0.743 |
Group A eukaryotes + Group B eukaryotes | Supplementary file 2 - tree 3 | 3.00E-37*** |
Group A1 eukaryotes: Blastocystis, Proteromonas, Neoparamoebids, Euglenids, Pygsuia | Supplementary file 2 - tree 4 | 0.622 |
Group A1 eukaryotes + Brevimastigamonas | Supplementary file 2 - tree 5 | 0.46 |
Group A1 eukaryotes + Brevimastigamonas + Mastigamoeba | Supplementary file 2 - tree 6 | 0.294 |
Group A eukaryotes | Supplementary file 2 - tree 7 | 0.253 |
Group B eukaryotes | Supplementary file 2 - tree 8 | 0.179 |
Obazoa (Pygsuia + Monosiga) | Supplementary file 2 - tree 9 | 0.002** |
Amoerphea (Obazoa + Amoebozoa) | Supplementary file 2 - tree 10 | 1.00E-32*** |
Amoebozoa | Supplementary file 2 - tree 11 | 0.206 |
Stramenopiles + Alveolates | Supplementary file 2 - tree 12 | 0.004** |
Stramenopiles + Alveolates + Rhizaria (SAR) | Supplementary file 2 - tree 13 | 0.034* |
Diaphoretickes (SAR + Euglenids) | Supplementary file 2 - tree 14 | 0.018* |
Rhizaria | Supplementary file 2 - tree 15 | 1.00E-60*** |
Eukaryotes + MAG alphaproteobacteria | Supplementary file 2 - tree 16 | 2.00E-41*** |
Group A eukaryotes + MAG alphaproteobacteria | Supplementary file 2 - tree 17 | 0.227 |
Alphaproteobacteria | Supplementary file 2 - tree 18 | 5.00E-34*** |
Eukaryotes + alphaproteobacteria | Supplementary file 2 - tree 19 | 8.00E-43*** |
Group A eukaryotes + Group A alphaproteobacteria | Supplementary file 2 - tree 20 | 3.00E-31*** |
Group B eukaryotes + Group B alphaproteobacteria | Supplementary file 2 - tree 21 | 4.00E-05*** |
Group A | ||
Maximum likelihood tree | Supplementary file 3 - tree 1 | 0.892 |
Eukaryotes | Supplementary file 3 - tree 2 | 0.225 |
Amoebozoa | Supplementary file 3 - tree 3 | 0.315 |
Pygsuia + Amoebozoa (Amorphea) | Supplementary file 3 - tree 4 | 0.22 |
Eukaryotes + alphaproteobacteria | Supplementary file 3 - tree 5 | 3.00E-59*** |
Eukaryotes + MAG alphaproteobacteria | Supplementary file 3 - tree 6 | 0.226 |
Group B | ||
Maximum likelihood tree | Supplementary file 4 - tree 1 | 0.827 |
Eukaryotes | Supplementary file 4 - tree 2 | 0.081 |
Stramenopiles + Alveolates | Supplementary file 4 - tree 3 | 0.287 |
SAR | Supplementary file 4 - tree 4 | 0.281 |
Eukaryotes + alphaproteobacteria | Supplementary file 4 - tree 5 | 2.00E-75*** |
aitalicized values indicate topologies that could not be rejected (p<0.05).
* 0.05 > p > 0.01
** 0.01 > p > 0.001
*** p < 0.001
Topology test output from CONSEL.
Trees 1-20 represent trees 2-21 from Supplementary file 2; trees 21-120 represent 100 bootstrap trees from the maximum likelihood analysis. Relevant column headers: Obs, observed log-likelihood …
Topology test output from CONSEL.
Trees 1-6 represent trees1-6 from Supplementary file 3; trees 7-106 represent 100 bootstrap trees from the maximum likelihood analysis. Relevant column headers: Obs, observed log-likelihood value; au, topology test p-value; np, bootstrap probability. Details on the column headers can be found at http://stat.sys.i.kyoto-u.ac.jp/prog/consel/quick.html
Topology test output from CONSEL.
Trees 1-5 represent trees 1-5 from Supplementary file 4; trees 6-105 represent 100 bootstrap trees from the maximum likelihood analysis. Relevant column headers: Obs, observed log-likelihood value; au, topology test p-value; np, bootstrap probability. Details on the column headers can be found at http://stat.sys.i.kyoto-u.ac.jp/prog/consel/quick.html
RquA detecteda | NCBI Genomesb | NCIB TSA nrc | MMETSPd | |
Alveolata | 7 | 105 | 32 | 134 |
Amoebozoa | 4 | 41 | 10 | 8 |
Apusozoa | 0 | 1 | 0 | 0 |
Breviatea | 1 | 1 | 1 | 0 |
Centroheliozoa | 0 | 0 | 1 | 0 |
Cryptophyta | 0 | 8 | 1 | 25 |
Euglenozoa | 2e | 55 | 3 | 5 |
Fornicata | 0 | 2 | 2 | 0 |
Glaucocystophyceae | 0 | 4 | 0 | 3 |
Haptophyceae | 0 | 5 | 2 | 61 |
Heterolobosea | 0 | 5 | 1 | 2 |
Jakobida | 0 | 6 | 0 | 0 |
Malawimonadidae | 0 | 2 | 0 | 0 |
Opisthokonta | 1 | 9,240 | 1395 | 10 |
Oxymonadida | 0 | 1 | 1 | 0 |
Parabasalia | 0 | 2 | 1 | 0 |
Rhizaria | 4 | 12 | 4 | 21 |
Rhodophyta | 0 | 124 | 15 | 8 |
Stramenopiles | 5 | 150 | 49 | 279 |
Viridiplantae | 0 | 2,461 | 499 | 72 |
unclassified | 0 | 0 | 3 | 19 |
Multispecies with undefined taxa ID | 0 | 0 | 82 | 19 |
Total | 24 | 12225 | 2102 | 647 |
a Source: this study b Source: NCBI Taxonomy Browser, selecting “Genomes” – January 28, 2018 c Source NCBI Trace Archive for the transcriptome shotgun assembly database availble at https://www.ncbi.nlm.nih.gov/Traces/wgs/?term=tsa Taxonomy ID were extracted and taxonomy parsed with ete-toolkit. Only non-redundant taxonomy IDs are shown. d Source: iMicrobe; Taxonomy ID were extracted and taxonomy assigned with ete-toolkit. Only non-redundant taxonomy IDs are shown.e Three copies were identified in Eutriptiella and 1 in Euglena |
Excel file with workbooks containing information about the number of genomes surveyed, PFAM domains of putative RquA homologues, gene accession numbers for RquA and Q-utilizing proteins, mitochondrial targeting sequence information, redox half-potentials used for Figure 5, bacterial genes with and without linkage to respiratory complexes.
PDF with all the trees for the full RquA phylogenetic analysis and associated topology tests
PDF with all the tree for the Group A phylogenetic analysis and associated topology tests
PDF with all the tree for the Group B phylogenetic analysis and associated topology tests