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PreprintCC BYbioRxiv

Tandem repeats in methanogenic archaea and their viruses reveal a shared potential for rapid genomic diversification

  • S. Haiss
  • E. J. Skoog
  • J. Herbert
  • C. Ding
  • K. Weidenbach
  • M. A. Tufail
  • S. Schlaich
  • B. Molitor
  • R. A. Schmitz
  • M. C. Schoelmerich1
  1. 1Environmental Microbiology, Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland
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Abstract

Methanogenic archaea drive global methane emissions, yet the molecular basis of their physiological flexibility is unclear. Archaeal adaptation is typically attributed to horizontal gene transfer, which is episodic and cannot explain rapid, reversible change. Here we show that direct tandem repeats (TRs) offer an intrinsic alternative. By screening 50,567 prokaryotic genomes, we find TR densities in Methanosarcina more than 30-fold above the prokaryotic average, paralleling Borg extrachromosomal elements. These TRs recur at conserved loci while sharing almost no sequence identity between strains, indicating independent origin, and evolve during routine cultivation. Methanogen TRs are transcribed, show ribosome occupancy, and lie near regulatory and cofactor-related genes, whilst being depleted around core energy-conserving and translational machinery. Genic TRs generate intrinsically disordered regions in proteins carrying nucleotide-binding, protein-protein interaction and cell-surface domains, and occur in structural and surface proteins of methanogen-infecting viruses. TRs are therefore an overlooked source of variability and adaptation potential in methanogens and their viruses.

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Cite

BibTeXRIS
BibTeX
@misc{haiss2026tandem,
  title = {{Tandem repeats in methanogenic archaea and their viruses reveal a shared potential for rapid genomic diversification}},
  author = {S. Haiss and E. J. Skoog and J. Herbert and C. Ding and K. Weidenbach and M. A. Tufail and S. Schlaich and B. Molitor and R. A. Schmitz and M. C. Schoelmerich},
  howpublished = {bioRxiv},
  year = {2026},
  month = oct,
  doi = {10.64898/2026.10.30.763056},
  url = {https://www.biorxiv.org/content/10.64898/2026.10.30.763056v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Tandem repeats in methanogenic archaea and their viruses reveal a shared potential for rapid genomic diversification
AU  - S. Haiss
AU  - E. J. Skoog
AU  - J. Herbert
AU  - C. Ding
AU  - K. Weidenbach
AU  - M. A. Tufail
AU  - S. Schlaich
AU  - B. Molitor
AU  - R. A. Schmitz
AU  - M. C. Schoelmerich
PY  - 2026
DA  - 2026/10/30
PB  - bioRxiv
DO  - 10.64898/2026.10.30.763056
UR  - https://www.biorxiv.org/content/10.64898/2026.10.30.763056v1
AB  - Methanogenic archaea drive global methane emissions, yet the molecular basis of their physiological flexibility is unclear. Archaeal adaptation is typically attributed to horizontal gene transfer, which is episodic and cannot explain rapid, reversible change. Here we show that direct tandem repeats (TRs) offer an intrinsic alternative. By screening 50,567 prokaryotic genomes, we find TR densities in Methanosarcina more than 30-fold above the prokaryotic average, paralleling Borg extrachromosomal elements. These TRs recur at conserved loci while sharing almost no sequence identity between strains, indicating independent origin, and evolve during routine cultivation. Methanogen TRs are transcribed, show ribosome occupancy, and lie near regulatory and cofactor-related genes, whilst being depleted around core energy-conserving and translational machinery. Genic TRs generate intrinsically disordered regions in proteins carrying nucleotide-binding, protein-protein interaction and cell-surface domains, and occur in structural and surface proteins of methanogen-infecting viruses. TRs are therefore an overlooked source of variability and adaptation potential in methanogens and their viruses.
ER  -