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  • 1
    Publication Date: 2015-05-07
    Description: The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4444528/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4444528/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spang, Anja -- Saw, Jimmy H -- Jorgensen, Steffen L -- Zaremba-Niedzwiedzka, Katarzyna -- Martijn, Joran -- Lind, Anders E -- van Eijk, Roel -- Schleper, Christa -- Guy, Lionel -- Ettema, Thijs J G -- 310039/European Research Council/International -- England -- Nature. 2015 May 14;521(7551):173-9. doi: 10.1038/nature14447. Epub 2015 May 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden. ; Department of Biology, Centre for Geobiology, University of Bergen, N-5020 Bergen, Norway. ; 1] Department of Biology, Centre for Geobiology, University of Bergen, N-5020 Bergen, Norway [2] Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria. ; 1] Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden [2] Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25945739" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/metabolism ; Actins/genetics/metabolism ; Archaea/*classification/genetics/metabolism ; Arctic Regions ; Endosomal Sorting Complexes Required for Transport/genetics/metabolism ; Eukaryota/*classification/genetics/metabolism ; Eukaryotic Cells/classification/metabolism ; *Evolution, Molecular ; Hydrothermal Vents/*microbiology ; Metagenome/genetics ; Molecular Sequence Data ; Monomeric GTP-Binding Proteins/genetics/metabolism ; *Phylogeny ; Prokaryotic Cells/*classification ; Proteome/genetics/isolation & purification/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2008-07-19
    Description: Berg et al. (Reports, 14 December 2007, p. 1782) reported the discovery of an autotrophic carbon dioxide-fixation pathway in Archaea and implicated a substantial role of this pathway in global carbon cycling based on sequence analysis of Global Ocean Sampling data. We question the validity of the latter claim.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ettema, Thijs J G -- Andersson, Siv G E -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):342; author reply 342. doi: 10.1126/science.1158766.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, S-752 36 Sweden. thijs.ettema@ebc.uu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635779" target="_blank"〉PubMed〈/a〉
    Keywords: Archaea/classification/genetics/*metabolism ; Autotrophic Processes ; Bacteria, Anaerobic/classification/genetics/metabolism ; Carbon Dioxide/*metabolism ; Hydro-Lyases/chemistry/*genetics/*metabolism ; Hydroxybutyrates/*metabolism ; Lactic Acid/*analogs & derivatives/metabolism ; Metabolic Networks and Pathways ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2016-02-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ettema, Thijs J G -- England -- Nature. 2016 Mar 3;531(7592):39-40. doi: 10.1038/nature16876. Epub 2016 Feb 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26840482" target="_blank"〉PubMed〈/a〉
    Keywords: Eukaryotic Cells/*cytology ; Genes, Bacterial/*genetics ; Genes, Mitochondrial/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Prokaryotic Cells/*cytology ; Symbiosis/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2016-05-17
    Description: In contrast to prokaryotes, eukaryotic cells are characterized by a complex set of internal membrane-bound compartments. A subset of these, and the protein machineries that move material between them, define the membrane-trafficking system (MTS), the emergence of which represents a landmark in eukaryotic evolution. Unlike mitochondria and plastids, MTS organelles have autogenous origins. Much of the MTS machinery is composed of building blocks, including small GTPase, coiled-coil, beta-propeller + alpha-solenoid, and longin domains. Despite the identification of prokaryotic proteins containing these domains, only few represent direct orthologues, leaving the origins and early evolution of the MTS poorly understood. Here, we present an in-depth analysis of MTS building block homologues in the composite genome of Lokiarchaeum, the recently discovered archaeal sister clade of eukaryotes, yielding several key insights. We identify two previously unreported Eukaryotic Signature Proteins; orthologues of the Gtr/Rag family GTPases, involved in target of rapamycin complex signaling, and of the RLC7 dynein component. We could not identify golgin or SNARE (coiled-coil) or beta-propeller + alpha-solenoid orthologues, nor typical MTS domain fusions, suggesting that these either were lost from Lokiarchaeum or emerged later in eukaryotic evolution. Furthermore, our phylogenetic analyses of lokiarchaeal GTPases support a split into Ras-like and Arf-like superfamilies, with different prokaryotic antecedents, before the advent of eukaryotes. While no GTPase activating proteins or exchange factors were identified, we show that Lokiarchaeum encodes numerous roadblock domain proteins and putative longin domain proteins, confirming the latter’s origin from Archaea. Altogether, our study provides new insights into the emergence and early evolution of the eukaryotic membrane-trafficking system.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 5
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-11
    Description: About 40 years ago, Archaea were recognized as a major prokaryotic domain of life besides Bacteria. Recently, cultivation-independent sequencing methods have produced a wealth of genomic data for previously unidentified archaeal lineages, several of which appear to represent newly revealed branches in the tree of life. Analyses of some recently obtained genomes have uncovered previously unknown metabolic traits and provided insights into the evolution of archaea and their relationship to eukaryotes. On the basis of our current understanding, much archaeal diversity still defies genomic exploration. Efforts to obtain and study genomes and enrichment cultures of uncultivated microbial lineages will likely further expand our knowledge about archaeal phylogenetic and metabolic diversity and their cell biology and ecological function.
    Keywords: Evolution, Online Only
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2008-04-23
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 7
    Publication Date: 2011-09-07
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 8
    Publication Date: 2008-11-05
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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