Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya

Jonathan Filée (), Hubert F. Becker, Lucille Mellottee, Rima Zein Eddine, Zhihui Li, Wenlu Yin, Jean-Christophe Lambry, Ursula Liebl and Hannu Myllykallio ()
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Jonathan Filée: Université Paris-Saclay
Hubert F. Becker: Ecole Polytechnique, Institut polytechnique de Paris
Lucille Mellottee: Ecole Polytechnique, Institut polytechnique de Paris
Rima Zein Eddine: Ecole Polytechnique, Institut polytechnique de Paris
Zhihui Li: Ecole Polytechnique, Institut polytechnique de Paris
Wenlu Yin: Ecole Polytechnique, Institut polytechnique de Paris
Jean-Christophe Lambry: Ecole Polytechnique, Institut polytechnique de Paris
Ursula Liebl: Ecole Polytechnique, Institut polytechnique de Paris
Hannu Myllykallio: Ecole Polytechnique, Institut polytechnique de Paris

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured ‘Candidatus Prometheoarchaeum syntrophicum’. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.

Date: 2023
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DOI: 10.1038/s41467-023-36487-z

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