Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, ... View Full Text


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Article Info

DATE

2013-04-22

AUTHORS

Mircea Podar, Kira S Makarova, David E Graham, Yuri I Wolf, Eugene V Koonin, Anna-Louise Reysenbach

ABSTRACT

BACKGROUND: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. RESULTS: The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. CONCLUSIONS: Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships. REVIEWERS: This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia. More... »

PAGES

9-9

References to SciGraph publications

  • 2008-02-08. The RAST Server: Rapid Annotations using Subsystems Technology in BMC GENOMICS
  • 2012-12-14. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer in BIOLOGY DIRECT
  • 2011-09-18. De novo assembly of bacterial genomes from single cells in NATURE BIOTECHNOLOGY
  • 2011-05-09. Evolution and classification of the CRISPR–Cas systems in NATURE REVIEWS MICROBIOLOGY
  • 2004-09-14. Composition of the lipids of Nanoarchaeum equitans and their origin from its host Ignicoccus sp. strain KIN4/I in ARCHIVES OF MICROBIOLOGY
  • 2007-01-15. Prediction of effective genome size in metagenomic samples in GENOME BIOLOGY
  • 2005-02. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves in NATURE
  • 2007-11-27. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea in BIOLOGY DIRECT
  • 2002-05. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont in NATURE
  • 2008-05. Life without RNase P in NATURE
  • 2012-02-13. The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes in BIOLOGY DIRECT
  • 2012-08-14. Genomic sequencing of uncultured microorganisms from single cells in NATURE REVIEWS MICROBIOLOGY
  • 2009-09-17. Formal Proof that the Split Genes of tRNAs of Nanoarchaeum equitans Are an Ancestral Character in JOURNAL OF MOLECULAR EVOLUTION
  • 2012-07-18. RNA processing in the minimal organism Nanoarchaeum equitans in GENOME BIOLOGY
  • 2011-09-13. Functional curation of the Sulfolobus solfataricus P2 and S. acidocaldarius 98-3 complete genome sequences in EXTREMOPHILES
  • 2004-02-26. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox in GENOME BIOLOGY
  • 2008-11-10. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans in GENOME BIOLOGY
  • 2008-07-12. Ignicoccus hospitalis and Nanoarchaeum equitans: ultrastructure, cell–cell interaction, and 3D reconstruction from serial sections of freeze-substituted cells and by electron cryotomography in ARCHIVES OF MICROBIOLOGY
  • 2008-06-14. Nanoarchaeal 16S rRNA gene sequences are widely dispersed in hyperthermophilic and mesophilic halophilic environments in EXTREMOPHILES
  • 2005-04-14. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? in GENOME BIOLOGY
  • Identifiers

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    http://scigraph.springernature.com/pub.10.1186/1745-6150-8-9

    DOI

    http://dx.doi.org/10.1186/1745-6150-8-9

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/23607440


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    38 schema:description BACKGROUND: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. RESULTS: The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. CONCLUSIONS: Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships. REVIEWERS: This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia.
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