ATP synthase evolution on a cross-braced dated tree of life

Tara A. Mahendrarajah, Edmund R. R. Moody, Dominik Schrempf, Lénárd L. Szánthó, Nina Dombrowski, Adrián A. Davín, Davide Pisani, Philip C. J. Donoghue, Gergely J. Szöllősi, Tom A. Williams () and Anja Spang ()
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Tara A. Mahendrarajah: NIOZ, Royal Netherlands Institute for Sea Research
Edmund R. R. Moody: University of Bristol
Dominik Schrempf: Eötvös University
Lénárd L. Szánthó: Eötvös University
Nina Dombrowski: NIOZ, Royal Netherlands Institute for Sea Research
Adrián A. Davín: The University of Tokyo
Davide Pisani: University of Bristol
Philip C. J. Donoghue: University of Bristol
Gergely J. Szöllősi: Eötvös University
Tom A. Williams: University of Bristol
Anja Spang: NIOZ, Royal Netherlands Institute for Sea Research

Nature Communications, 2023, vol. 14, issue 1, 1-18

Abstract: Abstract The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.

Date: 2023
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DOI: 10.1038/s41467-023-42924-w

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