Transcriptional landscape of the cell cycle in a model thermoacidophilic archaeon reveals similarities to eukaryotes

Miguel V. Gomez-Raya-Vilanova, Jérôme Teulière, Sofia Medvedeva, Yuping Dai, Eduardo Corel, Philippe Lopez, François-Joseph Lapointe, Debashish Bhattacharya, Louis-Patrick Haraoui, Elodie Turc, Marc Monot, Virginija Cvirkaite-Krupovic, Eric Bapteste () and Mart Krupovic ()
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Miguel V. Gomez-Raya-Vilanova: Archaeal Virology Unit
Jérôme Teulière: Université Des Antilles
Sofia Medvedeva: Archaeal Virology Unit
Yuping Dai: Université Des Antilles
Eduardo Corel: Université Des Antilles
Philippe Lopez: Université Des Antilles
François-Joseph Lapointe: Université de Montréal
Debashish Bhattacharya: Rutgers University
Louis-Patrick Haraoui: Université de Sherbrooke
Elodie Turc: Plate-forme Technologique Biomics
Marc Monot: Plate-forme Technologique Biomics
Virginija Cvirkaite-Krupovic: Archaeal Virology Unit
Eric Bapteste: Université Des Antilles
Mart Krupovic: Archaeal Virology Unit

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract Similar to many eukaryotes, the thermoacidophilic archaeon Saccharolobus islandicus follows a defined cell cycle program, with two growth phases, G1 and G2, interspersed by a chromosome replication phase (S), and followed by genome segregation and cytokinesis (M-D) phases. To study whether and which other processes are cell cycle-coordinated, we synchronized cultures of S. islandicus and performed an in-depth transcriptomic analysis of samples enriched in cells undergoing the M-G1, S, and G2 phases, providing a holistic view of the S. islandicus cell cycle. We show that diverse metabolic pathways, protein synthesis, cell motility and even antiviral defense systems, are expressed in a cell cycle-dependent fashion. Moreover, application of a transcriptome deconvolution method defined sets of phase-specific signature genes, whose peaks of expression roughly matched those of yeast homologs. Collectively, our data elucidates the complexity of the S. islandicus cell cycle, suggesting that it more closely resembles the cell cycle of certain eukaryotes than previously appreciated.

Date: 2025
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DOI: 10.1038/s41467-025-60613-8

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