Genomes of six viruses that infect Asgard archaea from deep-sea sediments - PubMed (original) (raw)

Genomes of six viruses that infect Asgard archaea from deep-sea sediments

Ian M Rambo et al. Nat Microbiol. 2022 Jul.

Abstract

Asgard archaea are globally distributed prokaryotic microorganisms related to eukaryotes; however, viruses that infect these organisms have not been described. Here, using metagenome sequences recovered from deep-sea hydrothermal sediments, we characterize six relatively large (up to 117 kb) double-stranded DNA (dsDNA) viral genomes that infected two Asgard archaeal phyla, Lokiarchaeota and Helarchaeota. These viruses encode Caudovirales-like structural proteins, as well as proteins distinct from those described in known archaeal viruses. Their genomes contain around 1-5% of genes associated with eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs) and appear to be capable of semi-autonomous genome replication, repair, epigenetic modifications and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. Genomic analysis of these Asgard viruses reveals that they contain features of both prokaryotic and eukaryotic viruses, and provides insights into their potential infection and host interaction mechanisms.

© 2022. The Author(s), under exclusive licence to Springer Nature Limited.

PubMed Disclaimer

Comment in

• A trove of Asgard archaeal viruses.
  Alarcón-Schumacher T, Erdmann S. Alarcón-Schumacher T, et al. Nat Microbiol. 2022 Jul;7(7):931-932. doi: 10.1038/s41564-022-01148-2. Nat Microbiol. 2022. PMID: 35760838 No abstract available.

Similar articles

• Three families of Asgard archaeal viruses identified in metagenome-assembled genomes.
  Medvedeva S, Sun J, Yutin N, Koonin EV, Nunoura T, Rinke C, Krupovic M. Medvedeva S, et al. Nat Microbiol. 2022 Jul;7(7):962-973. doi: 10.1038/s41564-022-01144-6. Epub 2022 Jun 27. Nat Microbiol. 2022. PMID: 35760839 Free PMC article.
• Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of _Loki_- and Thorarchaeota.
  Manoharan L, Kozlowski JA, Murdoch RW, Löffler FE, Sousa FL, Schleper C. Manoharan L, et al. mBio. 2019 Sep 10;10(5):e02039-19. doi: 10.1128/mBio.02039-19. mBio. 2019. PMID: 31506313 Free PMC article.
• Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea.
  Garg SG, Kapust N, Lin W, Knopp M, Tria FDK, Nelson-Sathi S, Gould SB, Fan L, Zhu R, Zhang C, Martin WF. Garg SG, et al. Genome Biol Evol. 2021 Jan 7;13(1):evaa238. doi: 10.1093/gbe/evaa238. Genome Biol Evol. 2021. PMID: 33462601 Free PMC article.
• Mythical origins of the actin cytoskeleton.
  Akıl C, Kitaoku Y, Tran LT, Liebl D, Choe H, Muengsaen D, Suginta W, Schulte A, Robinson RC. Akıl C, et al. Curr Opin Cell Biol. 2021 Feb;68:55-63. doi: 10.1016/j.ceb.2020.08.011. Epub 2020 Oct 10. Curr Opin Cell Biol. 2021. PMID: 33049465 Review.
• Asgard archaea in saline environments.
  Banciu HL, Gridan IM, Zety AV, Baricz A. Banciu HL, et al. Extremophiles. 2022 Jun 28;26(2):21. doi: 10.1007/s00792-022-01266-z. Extremophiles. 2022. PMID: 35761090 Review.

Cited by

• A metagenomic catalogue of the ruminant gut archaeome.
  Mi J, Jing X, Ma C, Shi F, Cao Z, Yang X, Yang Y, Kakade A, Wang W, Long R. Mi J, et al. Nat Commun. 2024 Nov 7;15(1):9609. doi: 10.1038/s41467-024-54025-3. Nat Commun. 2024. PMID: 39505912 Free PMC article.
• Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum.
  Wu Z, Liu S, Ni J. Wu Z, et al. Nat Microbiol. 2024 Dec;9(12):3362-3375. doi: 10.1038/s41564-024-01839-y. Epub 2024 Oct 24. Nat Microbiol. 2024. PMID: 39448846
• Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements.
  Valentin-Alvarado LE, Shi LD, Appler KE, Crits-Christoph A, De Anda V, Adler BA, Cui ML, Ly L, Leão P, Roberts RJ, Sachdeva R, Baker BJ, Savage DF, Banfield JF. Valentin-Alvarado LE, et al. Genome Res. 2024 Oct 29;34(10):1595-1609. doi: 10.1101/gr.279480.124. Genome Res. 2024. PMID: 39406503 Free PMC article.
• Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles.
  Nishikawa Y, Wagatsuma R, Tsukada Y, Chia-Ling L, Chijiiwa R, Hosokawa M, Takeyama H. Nishikawa Y, et al. ISME J. 2024 Jan 8;18(1):wrae124. doi: 10.1093/ismejo/wrae124. ISME J. 2024. PMID: 38976038 Free PMC article.
• The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis.
  Zhou Z, Liu Y, Anantharaman K, Li M. Zhou Z, et al. mLife. 2022 Dec 18;1(4):374-381. doi: 10.1002/mlf2.12048. eCollection 2022 Dec. mLife. 2022. PMID: 38818484 Free PMC article.

References

1. 1. Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015). - PubMed - PMC - DOI
2. 1. Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). - PubMed - DOI
3. 1. Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017). - PubMed - DOI
4. 1. Baker, B. J. et al. Diversity, ecology and evolution of Archaea. Nat. Microbiol. 5, 887–900 (2020). - PubMed - DOI
5. 1. Imachi, H. et al. Isolation of an archaeon at the prokaryote–eukaryote interface. Nature 577, 519–525 (2020). - PubMed - PMC - DOI

Publication types

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Nature Publishing Group