uu.seUppsala universitets publikasjoner
Endre søk
Begrens søket
1 - 4 of 4
RefereraExporteraLink til resultatlisten
Permanent link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Treff pr side
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sortering
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
Merk
Maxantalet träffar du kan exportera från sökgränssnittet är 250. Vid större uttag använd dig av utsökningar.
  • 1.
    Caceres, Eva F.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Genomic and evolutionary exploration of Asgard archaea2019Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Current evolutionary theories postulate that eukaryotes emerged from the symbiosis of an archaeal host with, at least, one bacterial symbiont. However, our limited grasp of microbial diversity hampers insights into the features of the prokaryotic ancestors of eukaryotes. This thesis focuses on the study of a group of uncultured archaea to better understand both existing archaeal diversity and the origin of eukaryotes.

    In a first study, we used short-read metagenomic approaches to obtain eight genomes of Lokiarchaeum relatives. Using these data we described the Asgard superphylum, comprised of at least four different phyla: Lokiarchaeota, Odinarchaeota, Thorarchaeota and Heimdallarchaoeta. Phylogenetic analyses suggested that eukaryotes affiliate with the Asgard group, albeit the exact position of eukaryotes with respect to Asgard archaea members remained inconclusive. Comparative genomics showed that Asgard archaea genomes encoded homologs of numerous eukaryotic signature proteins (ESPs), which had never been observed in Archaea before. Among these, there were several components of proteins involved in vesicle formation and membrane remodelling.

    In a second study, we used similar approaches to uncover additional members of the Asgard superphylum. Based on genome-centric metagenomics we recovered 69 new genomes from which we identified five additional candidate phyla: Freyarchaeota, Baldrarchaeota, Gefionarchaeota, Friggarchaeota and Idunnarchaeota. In this expanded dataset we could detect additional homologs for unreported ESPs. Updated phylogenies showed support for a scenario in which eukaryotes emerged from within Asgard archaea.

    We further took advantage of the increased Asgard diversity to delimit the gene content of the last common archaeal ancestor of eukaryotes using ancestral reconstruction analyses. The results suggest that the archaeal host cell who gave rise to eukaryotes already contained many of the genes associated with eukaryotic cellular complexity. Based on these analyses, we discussed the metabolic capabilities of the archaeal ancestor of eukaryotes.

    Finally, we reconstructed several nearly complete Lokiarchaeota genomes, one of them in only three contigs, using both short- and long-read metagenomics. These analyses indicate that long-read metagenomics is a promising approach to obtain highly complete and contiguous genomes directly from environmental samples, even from complex populations in the presence of microdiversity and low abundant members. This study further supports that the presence of ESPs in Asgard genomes is not the result of assembly and binning artefacts. 

    In conclusion, this thesis highlights the value of using culture-independent approaches together with phylogenomics and comparative genomics to improve our understanding of microbial diversity and to shed light into relevant evolutionary questions.

    Delarbeid
    1. Asgard archaea illuminate the origin of eukaryotic cellular complexity
    Åpne denne publikasjonen i ny fane eller vindu >>Asgard archaea illuminate the origin of eukaryotic cellular complexity
    Vise andre…
    2017 (engelsk)Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 541, nr 7637, s. 353-+Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.

    sted, utgiver, år, opplag, sider
    NATURE PUBLISHING GROUP, 2017
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-319133 (URN)10.1038/nature21031 (DOI)000396128800034 ()28077874 (PubMedID)
    Forskningsfinansiär
    Swedish Research Council, 2015-04959Knut and Alice Wallenberg FoundationEU, European Research Council, 310039-PUZZLE_CELL 294200-MICROENERGY 331291Swedish Foundation for Strategic Research , SSF-FFL5
    Tilgjengelig fra: 2017-04-03 Laget: 2017-04-03 Sist oppdatert: 2019-09-26bibliografisk kontrollert
    2. Expanded diversity of Asgard archaea points to Idunnarchaeota as closest relatives of eukaryotes
    Åpne denne publikasjonen i ny fane eller vindu >>Expanded diversity of Asgard archaea points to Idunnarchaeota as closest relatives of eukaryotes
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-393590 (URN)
    Tilgjengelig fra: 2019-09-25 Laget: 2019-09-25 Sist oppdatert: 2019-09-26
    3. Ancestral reconstruction of Asgard archaea provides insight into the gene content of the archaeal ancestor of eukaryotes
    Åpne denne publikasjonen i ny fane eller vindu >>Ancestral reconstruction of Asgard archaea provides insight into the gene content of the archaeal ancestor of eukaryotes
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-393589 (URN)
    Tilgjengelig fra: 2019-09-25 Laget: 2019-09-25 Sist oppdatert: 2019-09-26
    4. Reconstruction of a near-complete Lokiarchaeota genome using long- and short-read metagenomics of complex sediment samples
    Åpne denne publikasjonen i ny fane eller vindu >>Reconstruction of a near-complete Lokiarchaeota genome using long- and short-read metagenomics of complex sediment samples
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-393111 (URN)
    Tilgjengelig fra: 2019-09-25 Laget: 2019-09-25 Sist oppdatert: 2019-09-26
  • 2.
    Caceres, Eva F.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Wageningen University and Research, Department of Microbiology.
    Lewis, William H.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Wageningen University and Research, Department of Microbiology.
    Martin, Tom
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Homa, Felix
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Wageningen University and Research, Department of Microbiology.
    Schramm, Andreas
    Aarhus University, Section for Microbiology and Center for Geomicrobiology, Department of Bioscience.
    Kjeldsen, Kasper U.
    Aarhus University, Section for Microbiology and Center for Geomicrobiology, Department of Bioscience.
    Ettema, Thijs J. G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Wageningen University and Research, Department of Microbiology.
    Reconstruction of a near-complete Lokiarchaeota genome using long- and short-read metagenomics of complex sediment samplesManuskript (preprint) (Annet vitenskapelig)
  • 3.
    Eme, Laura
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Laboratoire Écologie, Systématique, Évolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech.
    Caceres, Eva F.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Wageningen University and Research, Laboratory of Microbiology.
    Tamarit, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Wageningen University and Research, Laboratory of Microbiology.
    Seitz, Kiley W.
    Dombrowski, Nina
    Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry.
    Homa, Felix
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Saw, Jimmy
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. George Washington University.
    Lombard, Jonathan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Li, Wen-Jun
    Hua, Zheng-Shuang
    Chen, Lin-Xing
    Banfield, Jillian
    Reysenbach, Anna-Louise
    Takuro, Nunoura
    Stott, Matthew B.
    Schramm, Andreas
    Kjeldsen, Kasper U.
    Baker, Brett J.
    Ettema, Thijs J. G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Wageningen University and Research, Laboratory of Microbiology.
    Expanded diversity of Asgard archaea points to Idunnarchaeota as closest relatives of eukaryotesManuskript (preprint) (Annet vitenskapelig)
  • 4.
    Fernandez Caceres, Eva
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Wageningen University and Research, Laboratory of Microbiology.
    Eme, Laura
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Laboratoire Écologie, Systématique, Évolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech.
    De Anda, Valerie
    Baker, Brett J.
    Ettema, Thijs J. G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Wageningen University and Research, Laboratory of Microbiology.
    Ancestral reconstruction of Asgard archaea provides insight into the gene content of the archaeal ancestor of eukaryotesManuskript (preprint) (Annet vitenskapelig)
1 - 4 of 4
RefereraExporteraLink til resultatlisten
Permanent link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf