Table 3. Other metabolic systems and traits analyzed in this work and their characteristics.
NADH, reduced form of nicotinamide adenine dinucleotide; TCA, Tricarboxylic acid cycle; ATP, adenosine 5′-triphosphate; FOF1, F0F1 ATP synthase; MICOS, Mitochondrial contact sites and cristae organizing system; SQMO, Squalene Monooxygenase; MRO, Mitochondria Related Organelle.
| Traits | Metabolic system | Reference | Taxonomic distribution and phylogenetic patterns for alphaproteobacteria (alpha) vs. eukaryotes | Iodidimonas |
|---|---|---|---|---|
| ≥16 | NADH-quinone oxidoreductase, complex I; TCA cycle also under anaerobiosis | (2, 8) | Already analyzed in previous works. The largest membrane subunits have strong phylogenetic signal but suffer from compositional artifacts due to their hydrophobicity. Other subunits have variable signals, with some too short for providing valuable phylogenies. Constitutively present in basically all alpha* | Yes |
| 5 | Succinate dehydrogenase, complex II; TCA cycle also under anaerobiosis | This work and (8) | Already analyzed in previous works. The two largest catalytic subunits have good phylogenetic signal, while the two membrane subunits are short and poorly conserved. Constitutively present in basically all alpha* | Yes |
| ≥12 | F0F1 ATP synthase | (8, 80) | Already analyzed in previous works. The largest catalytic subunits have strong phylogenetic signal, while most membrane subunits are short and poorly conserved. Constitutively present in all alpha* | Yes |
| 1 | ETF-Q dehydrogenase | This work | Monophyletic eukaryotic clade. Constitutively present in basically all alpha*. | Yes |
| 1 | Sulfite oxidase | This work | Monophyletic eukaryotic clade but localized in peroxisomes in Viridiplanta. Widely distributed among alphaproteobacteria. | Yes |
| 4 | [Fe-Fe]hydrogenase and its assembly factors - anaerobic metabolism | (25, 82) | The mature hydrogenase localizes in MRO and also the cytoplasm of various anaerobic eukaryotes, which might have acquired the traits via LGT from different bacteria. Very limited distribution in alpha. | No |
| 2 | NirBD for nitrate assimilation | (11) | The pathway is not localized in mitochondria. Predominantly present in Opistokhonts forming polyphyletic eukaryotic clades with intermixed bacteria. | No |
| 1 | Mic60 | This work and (8, 33) | Already analyzed in previous works. It may have a different function in bacteria (part of the hem operon) and mitochondria (part of the MICOS system regulating cristae). Poor conservation of bacterial proteins. | Yes |
| 2 | Ftsy and Fhp for membrane sorting | This work and (83) | Only Fhp produces a monophyletic eukaryotic clade. Distribution is limited to a small set of eukaryotes. | Yes |
| ≥8 | Aerobic biosynthesis of ubiquinone | This work and (51) | Proteins are poorly conserved and some have yet unrecognized eukaryotic counterparts. Both polyphyletic and monophyletic eukaryotic clades. Constitutively present in all alpha* without parasitic lifestyle. | Yes |
| ≥4 | Biosynthesis of sterols | This work and (10) | The pathway is not localized in mitochondria. SQMO catalyzes the first oxygen-dependent step but produces polyphyletic eukaryotic clades with intermixed bacteria. Moreover, this and other enzymes for sterol biosynthesis are scarcely present in alpha. | Partially |
| ≥4 | Biosynthesis of phospholipids: PC PI and PS | This work and (40) | The pathways are not localized in mitochondria and include members of the CDP-AT superfamily related to enzymes evaluated here for cardiolipin metabolism. Poor conservation between alpha and eukaryotes. Scattered distribution among alpha. | Partially |
| 1 | CTP synthase | (80) | Nonmonophyletic clade when most eukaryotes are considered. Constitutively present in most alpha*. | Yes |
| 4 | Nuclear encoded respiratory proteins, similarity by BLAST | This work and (58) | The eukaryotic proteins generally produce monophyletic clades. In this work, BLAST searches were computed for some proteins as described in Materials and Methods. The results of MPPbeta are presented in fig. S2C. | Yes |