Archaea articles within Nature Communications

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  • Article
    | Open Access

    The prokaryote defence system Dnd relies on phosphorothioation (PT) of DNA backbone to distinguish between self and non-self DNA. Here, Xiong et al. describe a previously uncharacterized PT-based antiviral system that is independent of the canonical Dnd and is widespread in Archaea and Bacteria.

    • Lei Xiong
    • , Siyi Liu
    •  & Shi Chen

  • Article
    | Open Access

    Cofactor F420 plays crucial roles in bacterial and archaeal metabolism, but its biosynthetic pathway is not fully understood. Here, the authors present the structure of one of the enzymes and provide experimental evidence for a substantial revision of the pathway, including the identification of a new intermediate.

    • Ghader Bashiri
    • , James Antoney
    •  & Colin J. Jackson

  • Article
    | Open Access

    Certain archaea appear to metabolize fatty acids, but the regulation of these pathways is unclear. Here, Wang et al. provide genetic, functional and structural evidence supporting that a TetR-family transcriptional regulator is involved in regulation of fatty acid metabolism in Sulfolobus acidocaldarius.

    • Kun Wang
    • , David Sybers
    •  & Eveline Peeters

  • Article
    | Open Access

    Chemosynthetic microbial communities in hydrothermal environments receiving meteoric and geothermal fluids are understudied. Here, Colman et al. use metagenomics to study one such community from a hot spring at Yellowstone National Park, revealing exceptional biodiversity and unique functional potential.

    • Daniel R. Colman
    • , Melody R. Lindsay
    •  & Eric S. Boyd

  • Article
    | Open Access

    Sulfolobus islandicus is a model organism within the TACK superphylum of the Archaea. Here, the authors perform a genome-wide analysis of essential genes in this organism, show that the proteinaceous S-layer is not essential, and explore potential stages of evolution of the essential gene repertoire in Archaea.

    • Changyi Zhang
    • , Alex P. R. Phillips
    •  & Rachel J. Whitaker

  • Article
    | Open Access

    The phylum of archaea Aigarchaeota is poorly characterized due to limited genomic sampling. Here, Hua and colleagues use genome-resolved metagenome sequencing to reconstruct six hot spring strains of Aigarchaeota and then infer their metabolism and evolutionary history.

    • Zheng-Shuang Hua
    • , Yan-Ni Qu
    •  & Wen-Jun Li

  • Article
    | Open Access

    Ubiquitin modification also occurs in archaea. Here, the authors characterize an archaeal ancestral ubiquitination system, present the crystal structure of the archaeal deubiquitinase Rpn11 from Caldiarchaeum subterraneum bound to ubiquitin and provide insights into evolutionary relationships.

    • Adrian C. D. Fuchs
    • , Lorena Maldoner
    •  & Jörg Martin

  • Article
    | Open Access

    Ammonia-oxidising archaea (AOA) were only discovered a little over a decade ago and remain poorly characterized despite their ubiquity and importance for nitrogen cycling. Here, the authors define a taxonomy of AOA based on a resolved amoA phylogeny and describe emergent global patterns in AOA diversity.

    • Ricardo J. Eloy Alves
    • , Bui Quang Minh
    •  & Christa Schleper

  • Article
    | Open Access

    Microbes in the cow rumen are crucial for the breakdown of plant material. Here, Stewart et al. assemble over 900 bacterial and archaeal genomes from the cow rumen microbiome, revealing new species and genes encoding enzymes with potential roles in carbohydrate metabolism.

    • Robert D. Stewart
    • , Marc D. Auffret
    •  & Mick Watson

  • Article
    | Open Access

    Many methanogenic archaea use H2 and CO2 to produce methane. Here, Taubner et al. show that Methanothermococcus okinawensis produces methane under conditions extrapolated for Saturn’s icy moon, Enceladus, and estimate that serpentinization may produce sufficient H2 for biological methane production.

    • Ruth-Sophie Taubner
    • , Patricia Pappenreiter
    •  & Simon K.-M. R. Rittmann

  • Article
    | Open Access

    Transcript cleavage factors such as eukaryotic TFIIS assist the resumption of transcription following RNA pol II backtracking. Here the authors find that one of the Sulfolobus solfataricus TFIIS homolog—TFS4—has evolved into a potent RNA polymerase inhibitor potentially involved in antiviral defense.

    • Thomas Fouqueau
    • , Fabian Blombach
    •  & Finn Werner

  • Article
    | Open Access

    The rod-shaped virus APBV1 is among the most thermostable viruses known. Here, Ptchelkine et al. determine its structure at near-atomic resolution, show that the DNA is packed as left-handed superhelix and identify extended hydrophobic interfaces that likely contribute to the extreme thermostability of the capsid.

    • Denis Ptchelkine
    • , Ashley Gillum
    •  & Juha T. Huiskonen

  • Article
    | Open Access

    In the absence of complete genomes, the metabolic capabilities of uncultured ARMAN-like archaea have been uncertain. Here, Golyshina et al. apply an enrichment culture technique and find that the ungapped genome of the ARMAN-like archaeon Mia14 has lost key metabolic pathways, suggesting dependence on the host archaeon Cuniculiplasma divulgatum.

    • Olga V. Golyshina
    • , Stepan V. Toshchakov
    •  & Peter N. Golyshin

  • Article
    | Open Access

    Activity-based protein profiling (ABPP) is a chemical proteomics method to profile activity states of enzymes under physiological conditions. Here the authors show that ABPP can be applied to archaeal serine hydrolases in the model organismSulfolobus acidocaldariusand can be used to identify novel putative serine hydrolases.

    • Susanne Zweerink
    • , Verena Kallnik
    •  & Markus Kaiser

  • Article
    | Open Access

    Although not photosynthetic, some archaea possess RuBisCO, one of the enzymes characteristic of the photosynthetic Calvin-Benson cycle, but apparently lack another one, phosphoribulokinase (PRK). Here the authors describe a carbon metabolic pathway in methanogenic archaea, involving RuBisCO and PRK.

    • Takunari Kono
    • , Sandhya Mehrotra
    •  & Hiroki Ashida

  • Article
    | Open Access

    How archaeal viruses perturb host transcription machinery is poorly understood. Here, the authors provide evidence that the archaeo-viral transcription factor ORF145/RIP targets host RNA polymerase, repressing its activity.

    • Carol Sheppard
    • , Fabian Blombach
    •  & Finn Werner

  • Article
    | Open Access

    Many microbial lineages have not yet been cultured, which hampers our understanding of their physiology. Here, Wurch et al. use single-cell genomics to infer cultivation conditions for the isolation of a tiny ectosymbiotic nanoarchaeon and its crenarchaeota host from a geothermal spring.

    • Louie Wurch
    • , Richard J. Giannone
    •  & Mircea Podar

  • Article
    | Open Access

    Archaea use multiple origins for chromosome replication, but some potential origins appear to be inactive during the genome replication. Here, Yang et al. show that when active origins are deleted from Haloferax mediterranei, a dormant origin is activated and essential, suggesting an origin-dependent replication.

    • Haibo Yang
    • , Zhenfang Wu
    •  & Hua Xiang

  • Article
    | Open Access

    Diversity-generating retroelements (DGRs) are genetic elements that introduce sequence variation within target genes in bacteria and their viruses. Here, Paul et al. report the discovery of DGRs in an archaeal virus and in two archaea from marine and terrestrial subsurface environments, respectively.

    • Blair G. Paul
    • , Sarah C. Bagby
    •  & David L. Valentine

  • Article |

    Little is known about certain bacterial phyla because of our current inability to grow them in the lab. Here, Luef et al.combine metagenomics and ultrastuctural analyses to show that some of these bacteria have a very small cell size, tightly packed DNA, few ribosomes and diverse pili-like structures.

    • Birgit Luef
    • , Kyle R. Frischkorn
    •  & Jillian F. Banfield

  • Article |

    Archaeal and eukaryotic RNA polymerases (RNAP) have conserved functional and structural similarities. Here, Jun et al.solve the first structure of a euryarchaeal RNAP in the open clamp conformation and identify insertions that may have evolved in eukaryotic Pol II to bind unique transcription factors.

    • Sung-Hoon Jun
    • , Akira Hirata
    •  & Katsuhiko S. Murakami

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