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  • 151.
    Parducci, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Alsos, Inger Greve
    Univ Tromso, Arctic Univ Norway, Tromso Museum, Tromso, Norway.
    Unneberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pedersen, Mikkel W.
    Univ Cambridge, Dept Zool, Cambridge, England.
    Han, Lu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Jilin Univ, Ancient DNA Lab, Coll Life Sci, Changchun, Jilin, Peoples R China.
    Lammers, Youri
    Univ Tromso, Arctic Univ Norway, Tromso Museum, Tromso, Norway.
    Salonen, J. Sakari
    Univ Helsinki, Dept Geosci & Geog, Helsinki, Finland.
    Valiranta, Minna M.
    Univ Helsinki, Ecosyst & Environm Res Programme, ECRU, Helsinki, Finland.
    Slotte, Tanja
    Stockholm Univ, Dept Ecol Environm & Plant Sci, Stockholm, Sweden;Sci Life Lab, Solna, Sweden.
    Wohlfarth, Barbara
    Stockholm Univ, Dept Geol Sci, Stockholm, Sweden;Stockholm Univ, Bolin Ctr Climate Res, Stockholm, Sweden.
    Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden2019In: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 7, article id 189Article in journal (Refereed)
    Abstract [en]

    The lake sediments of Hasseldala Port in south-east Sweden provide an archive of local and regional environmental conditions similar to 14.5-9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerod (14.1-12.7 ka BP), Younger Dryas (12.7-11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerod; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach.

  • 152.
    Peirasmaki, Dimitra
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Ma'ayeh, Showgy Y.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Xu, Feifei
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Ferella, Marcela
    Eukaryotic Single Cell Genomics Platform, Karolinska Institute, SciLifeLab, Sweden.
    Campos, Sara
    Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.
    Liu, Jingyi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Svärd, Staffan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    High Cysteine Proteins are up-regulated during Giardia-host cell interaction.Manuscript (preprint) (Other academic)
  • 153.
    Pelve, Erik A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Unique Solutions to Universal Problems: Studies of the Archaeal Cell2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Archaea is one of the three domains of life and studies of archaeal biology are important for understanding of life in extreme environments, fundamental biogeochemical processes, the origin of life, the eukaryotic cell and their own, unique biology. This thesis presents four studies of the archaeal cell, using the extremophilic Sulfolobus and ocean living Nitrosopumilus as model systems.

    Cell division in crenarchaea is shown to be carried out by a previously unknown system named Cdv (cell division). The system shares homology with the eukaryotic ESCRT-III system which is used for membrane reorganization during vesicle formation, viral release and cytokinesis. Organisms of the phylum Thaumarchaeota also use the Cdv system, despite also carrying genes for the euryarchaeal and bacterial cell division system FtsZ.

    The thaumarchaeal cell cycle is demonstrated to be dominated by the prereplicative and replicative stage, in contrasts to the crenarchaeal cell cycle where the cell at the majority of the time resides in the postreplicative stage. The replication rate is remarkably low and closer to what is measured for eukaryotes than other archaea.

    The gene organization of Sulfolobus is significantly associated with the three origins of replication. The surrounding regions are dense with genes of high importance for the organisms such as highly transcribed genes, genes with known function in fundamental cellular processes and conserved archaeal genes. The overall gene density is elevated and transposons are underrepresented.

    The archaeal virus SIRV2 displays a lytic life style where the host cell at the final stage of infection is disrupted for release of new virus particles. The remarkable pyramid-like structure VAP (virus associated pyramids), that is formed independently of the virus particle, is used for cell lysis.

    The research presented in this thesis describes unique features of the archaeal cell and influences our understanding of the entire tree of life.

    List of papers
    1. A unique cell division machinery in the Archaea
    Open this publication in new window or tab >>A unique cell division machinery in the Archaea
    Show others...
    2008 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 48, p. 18942-18946Article in journal (Refereed) Published
    Abstract [en]

    In contrast to the cell division machineries of bacteria, euryarchaea, and eukaryotes, no division components have been identified in the second main archaeal phylum, Crenarchaeota. Here, we demonstrate that a three-gene operon, cdv, in the crenarchaeon Sulfolobus acidocaldarius, forms part of a unique cell division machinery. The operon is induced at the onset of genome segregation and division, and the Cdv proteins then polymerize between segregating nucleoids and persist throughout cell division, forming a successively smaller structure during constriction. The cdv operon is dramatically down-regulated after UV irradiation, indicating division inhibition in response to DNA damage, reminiscent of eukaryotic checkpoint systems. The cdv genes exhibit a complementary phylogenetic range relative to FtsZ-based archaeal division systems such that, in most archaeal lineages, either one or the other system is present. Two of the Cdv proteins, CdvB and CdvC, display homology to components of the eukaryotic ESCRT-III sorting complex involved in budding of luminal vesicles and HIV-1 virion release, suggesting mechanistic similarities and a common evolutionary origin.

    Keywords
    cdv, Crenarchaeota, cytokinesis, ftsZ, Sulfolobus
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-106988 (URN)10.1073/pnas.0809467105 (DOI)000261489100060 ()
    Available from: 2009-07-15 Created: 2009-07-15 Last updated: 2017-12-13Bibliographically approved
    2. A unique virus release mechanism in the Archaea
    Open this publication in new window or tab >>A unique virus release mechanism in the Archaea
    Show others...
    2009 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 27, p. 11306-11311Article in journal (Refereed) Published
    Abstract [en]

    Little is known about the infection cycles of viruses infecting cells from Archaea, the third domain of life. Here, we demonstrate that the virions of the archaeal Sulfolobus islandicus rod-shaped virus 2 (SIRV2) are released from the host cell through a mechanism, involving the formation of specific cellular structures. Large pyramidal virus-induced protrusions transect the cell envelope at several positions, rupturing the S-layer; they eventually open out, thus creating large apertures through which virions escape the cell. We also demonstrate that massive degradation of the host chromosomes occurs because of virus infection, and that virion assembly occurs in the cytoplasm. Furthermore, intracellular viral DNA is visualized by flow cytometry. The results show that SIRV2 is a lytic virus, and that the host cell dies as a consequence of elaborated mechanisms orchestrated by the virus. The generation of specific cellular structures for a distinct step of virus life cycle is known in eukaryal virus-host systems but is unprecedented in cells from other domains.

    Keywords
    lysis, virus factory, hyperthermophile, infection cycle
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-128369 (URN)10.1073/pnas.0901238106 (DOI)000267796100079 ()
    Available from: 2010-07-22 Created: 2010-07-20 Last updated: 2017-12-12Bibliographically approved
    3. Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus
    Open this publication in new window or tab >>Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus
    Show others...
    2011 (English)In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 82, no 3, p. 555-566Article in journal (Refereed) Published
    Abstract [en]

    Cell division is mediated by different mechanisms in different evolutionary lineages. While bacteria and euryarchaea utilize an FtsZ-based mechanism, most crenarchaea divide using the Cdv system, related to the eukaryotic ESCRT-III machinery. Intriguingly, thaumarchaeal genomes encode both FtsZ and Cdv protein homologues, raising the question of their division mode. Here, we provide evidence indicating that Cdv is the primary division system in the thaumarchaeon Nitrosopumilus maritimus. We also show that the cell cycle is differently organized as compared to hyperthermophilic crenarchaea, with a longer pre-replication phase and a shorter post-replication stage. In particular, the time required for chromosome replication is remarkably extensive, 15-18 h, indicating a low replication rate. Further, replication did not continue to termination in a significant fraction of N. maritimus cell populations following substrate depletion. Both the low replication speed and the propensity for replication arrest are likely to represent adaptations to extremely oligotrophic environments. The results demonstrate that thaumarchaea, crenarchaea and euryarchaea display differences not only regarding phylogenetic affiliations and gene content, but also in fundamental cellular and physiological characteristics. The findings also have implications for evolutionary issues concerning the last archaeal common ancestor and the relationship between archaea and eukaryotes.

    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-162884 (URN)10.1111/j.1365-2958.2011.07834.x (DOI)000297282200004 ()21923770 (PubMedID)
    Available from: 2011-12-05 Created: 2011-12-05 Last updated: 2017-12-08Bibliographically approved
    4. Replication-biased genome organisation in the crenarchaeon Sulfolobus
    Open this publication in new window or tab >>Replication-biased genome organisation in the crenarchaeon Sulfolobus
    Show others...
    2010 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, p. 454-Article in journal (Refereed) Published
    Abstract [en]

    Background: Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. Results: We demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more highly expressed at all three origins. The bias by far exceeds what would be anticipated by gene dosage effects alone. In addition, early replicating regions are denser in archaeal core genes (enriched in essential functions), display lower intergenic distances, and are devoid of mobile genetic elements. Conclusion: The strong replication-biased structuring of the Sulfolobus chromosome implies that the multiple replication origins serve purposes other than simply shortening the time required for replication. The higher-level chromosomal organisation could be of importance for minimizing the impact of DNA damage, and may also be linked to transcriptional regulation.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-134173 (URN)10.1186/1471-2164-11-454 (DOI)000282787800003 ()
    Available from: 2010-11-22 Created: 2010-11-22 Last updated: 2017-12-12Bibliographically approved
  • 154.
    Pelve, Erik A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Fontanez, Kristina M.
    Fluid Screen Inc, Cambridge, MA USA;MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
    DeLong, Edward F.
    Univ Hawaii Manoa, Dept Oceanog, Daniel K Inoue Ctr Microbial Oceanog Res & Educ, Honolulu, HI 96822 USA.
    Bacterial Succession on Sinking Particles in the Ocean's Interior2017In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, article id 2269Article in journal (Refereed)
    Abstract [en]

    Sinking particles formed in the photic zone and moving vertically through the water column are a main mechanism for nutrient transport to the deep ocean, and a key component of the biological carbon pump. The particles appear to be processed by a microbial community substantially different from the surrounding waters. Single cell genomics and metagenomics were employed to describe the succession of dominant bacterial groups during particle processing. Sinking particles were extracted from sediment traps at Station Aloha in the North Pacific Subtropical Gyre (NPSG) during two different trap deployments conducted in July and August 2012. The microbial communities in poisoned vs. live sediment traps differed significantly from one another, consistent with prior observations by Fontanez et al. (2015). Partial genomes from these communities were sequenced from cells belonging to the genus Arcobacter (commensalists potentially associated with protists such as Radiolaria), and Vibrio carnpbellii (a group previously reported to be associated with crustacea). These bacteria were found in the particle-associated communities at specific depths in both trap deployments, presumably due to their specific host-associations. Partial genomes were also sequenced from cells belonging to Idiomarina and Kangiella that were enriched in live traps over a broad depth range, that represented a motile copiotroph and a putatively non-motile algicidal saprophyte, respectively. Planktonic bacterial cells most likely caught in the wake of the particles belonging to Actinomarina and the SAR11 Glade were also sequenced. Our results suggest that similar groups of eukaryote-associated bacteria are consistently found on sinking particles at different times, and that particle remineralization involves specific, reproducible bacterial succession events in oligotrophic ocean waters.

  • 155.
    Pelve, Erik A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Lindås, Ann-Christin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Knöppel, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Mira, Alex
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Four chromosome replication origins in the archaeon Pyrobaculum calidifontis2012In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 85, no 5, p. 986-995Article in journal (Refereed)
    Abstract [en]

    Replication origins were mapped in hyperthermophilic crenarchaea, using high-throughput sequencing-based marker frequency analysis. We confirm previous origin mapping in Sulfolobus acidocaldarius, and demonstrate that the single chromosome of Pyrobaculum calidifontis contains four replication origins, the highest number detected in a prokaryotic organism. The relative positions of the origins in both organisms coincided with regions enriched in highly conserved (core) archaeal genes. We show that core gene distribution provides a useful tool for origin identification in archaea, and predict multiple replication origins in a range of species. One of the P. calidifontis origins was mapped in detail, and electrophoretic mobility shift assays demonstrated binding of the Cdc6/Orc1 replication initiator protein to a repeated sequence element, denoted Orb-1, within the origin. The high-throughput sequencing approach also allowed for an annotation update of both genomes, resulting in the restoration of open reading frames encoding proteins involved in, e.g., sugar, nitrate and energy metabolism, as well as in glycosylation and DNA repair.

  • 156.
    Pelve, Erik A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Lindås, Ann-Christin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Martens-Habbena, Willm
    de la Torre, José R.
    Stahl, David A.
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus2011In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 82, no 3, p. 555-566Article in journal (Refereed)
    Abstract [en]

    Cell division is mediated by different mechanisms in different evolutionary lineages. While bacteria and euryarchaea utilize an FtsZ-based mechanism, most crenarchaea divide using the Cdv system, related to the eukaryotic ESCRT-III machinery. Intriguingly, thaumarchaeal genomes encode both FtsZ and Cdv protein homologues, raising the question of their division mode. Here, we provide evidence indicating that Cdv is the primary division system in the thaumarchaeon Nitrosopumilus maritimus. We also show that the cell cycle is differently organized as compared to hyperthermophilic crenarchaea, with a longer pre-replication phase and a shorter post-replication stage. In particular, the time required for chromosome replication is remarkably extensive, 15-18 h, indicating a low replication rate. Further, replication did not continue to termination in a significant fraction of N. maritimus cell populations following substrate depletion. Both the low replication speed and the propensity for replication arrest are likely to represent adaptations to extremely oligotrophic environments. The results demonstrate that thaumarchaea, crenarchaea and euryarchaea display differences not only regarding phylogenetic affiliations and gene content, but also in fundamental cellular and physiological characteristics. The findings also have implications for evolutionary issues concerning the last archaeal common ancestor and the relationship between archaea and eukaryotes.

  • 157.
    Ponce-de-Leon, Miguel
    et al.
    Univ Complutense Madrid, Fac Ciencias Quim, Dept Bioquim & Biol Mol 1, Madrid, Spain..
    Tamarit, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Calle-Espinosa, Jorge
    Univ Complutense Madrid, Fac Ciencias Quim, Dept Bioquim & Biol Mol 1, Madrid, Spain..
    Mori, Matteo
    Univ Calif San Diego, Dept Phys, La Jolla, CA 92093 USA..
    Latorre, Amparo
    Univ Valencia, Dept Genet, Valencia, Spain.;Univ Valencia, CSIC, Inst Integrat Syst Biol, Valencia, Spain..
    Montero, Francisco
    Univ Complutense Madrid, Fac Ciencias Quim, Dept Bioquim & Biol Mol 1, Madrid, Spain..
    Pereto, Juli
    Univ Valencia, CSIC, Inst Integrat Syst Biol, Valencia, Spain.;Univ Valencia, Dept Bioquim & Biol Mol, Valencia, Spain..
    Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium2017In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, article id 2290Article in journal (Refereed)
    Abstract [en]

    Bacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism-which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphid Cinara cedri that harbors two co-primary endosymbionts, Buchnera aphidicola BCc and Ca. Serratia symbiotica SCc, and in which some metabolic pathways are partitioned between different partners. Here we present a genome-scale metabolic network (GEM) for the bacterial consortium from the cedar aphid iBSCc. The analysis of this GEM allows us the confirmation of cases of metabolic complementation previously described by genome analysis (i.e., tryptophan and biotin biosynthesis) and the redefinition of an event of metabolic pathway sharing between the two endosymbionts, namely the biosynthesis of tetrahydrofolate. In silico knock-out experiments with iBSCc showed that the consortium metabolism is a highly integrated yet fragile network. We also have explored the evolutionary pathways leading to the emergence of metabolic complementation between reduced metabolisms starting from individual, complete networks. Our results suggest that, during the establishment of metabolic complementation in endosymbionts, adaptive evolution is significant in the case of tryptophan biosynthesis, whereas vitamin production pathways seem to adopt suboptimal solutions.

  • 158. Quebatte, Maxime
    et al.
    Dehio, Michaela
    Tropel, David
    Basler, Andrea
    Toller, Isabella
    Raddatz, Guenter
    Engel, Philipp
    Huser, Sonja
    Schein, Hermine
    Lindroos, Hillevi L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Molecular Evolution.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Molecular Evolution.
    Dehio, Christoph
    The BatR/BatS Two-Component Regulatory System Controls the Adaptive Response of Bartonella henselae during Human Endothelial Cell Infection2010In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 192, no 13, p. 3352-3367Article in journal (Refereed)
    Abstract [en]

    Here, we report the first comprehensive study of Bartonella henselae gene expression during infection of human endothelial cells. Expression of the main cluster of upregulated genes, comprising the VirB type IV secretion system and its secreted protein substrates, is shown to be under the positive control of the transcriptional regulator BatR. We demonstrate binding of BatR to the promoters of the virB operon and a substrate-encoding gene and provide biochemical evidence that BatR and BatS constitute a functional two-component regulatory system. Moreover, in contrast to the acid-inducible (pH 5.5) homologs ChvG/ChvI of Agrobacterium tumefaciens, BatR/BatS are optimally activated at the physiological pH of blood (pH 7.4). By conservation analysis of the BatR regulon, we show that BatR/BatS are uniquely adapted to upregulate a genus-specific virulence regulon during hemotropic infection in mammals. Thus, we propose that BatR/BatS two-component system homologs represent vertically inherited pH sensors that control the expression of horizontally transmitted gene sets critical for the diverse host-associated life styles of the alphaproteobacteria.

  • 159.
    Raina, Jean-Baptiste
    et al.
    Univ Technol Sydney, Climate Change Cluster, Ultimo, NSW, Australia.
    Eme, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pollock, F. Joseph
    Penn State Univ, Dept Biol, Eberly Coll Sci, University Pk, PA USA.
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. NIOZ, Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, Netherlands; Univ Utrecht, Netherlands.
    Archibald, John M.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.
    Williams, Tom A.
    Univ Bristol, Sch Biol Sci, Bristol, Avon, England.
    Symbiosis in the microbial world: from ecology to genome evolution2018In: BIOLOGY OPEN, ISSN 2046-6390, Vol. 7, no 2, article id UNSP bio032524Article, review/survey (Refereed)
    Abstract [en]

    The concept of symbiosis - defined in 1879 by de Bary as 'the living together of unlike organisms' - has a rich and convoluted history in biology. In part, because it questioned the concept of the individual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, diverse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for example, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists' workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired.

  • 160. Reimann, Julia
    et al.
    Lassak, Kerstin
    Khadouma, Sunia
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Yang, Nuan
    Driessen, Arnold J. M.
    Klingl, Andreas
    Albers, Sonja-Verena
    Regulation of archaella expression by the FHA and von Willebrand domain-containing proteins ArnA and ArnB in Sulfolobus acidocaldarius2012In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 86, no 1, p. 24-36Article in journal (Refereed)
    Abstract [en]

    The ability of microorganisms to sense and respond to sudden changes in their environment is often based on regulatory systems comprising reversible protein phosphorylation. The archaellum (former: archaeal flagellum) is used for motility in Archaea and therefore functionally analogous to the bacterial flagellum. In contrast with archaellum-mediated movement in certain members of the Euryarchaeota, this process, including its regulation, remains poorly studied in crenarchaeal organisms like Sulfolobus species. Recently, it was shown in Sulfolobus acidocaldarius that tryptone limiting conditions led to the induction of archaella expression and assembly. Here we have identified two proteins, the FHA domain-containing protein ArnA and the vWA domain-containing protein ArnB that are involved in regulating archaella expression in S. acidocaldarius. Both proteins are phosphorylated by protein kinases in vitro and interact strongly in vivo. Phenotypic analyses revealed that these two proteins are repressors of archaella expression. These results represent the first step in understanding the networks that underlie regulation of cellular motility in Crenarchaeota and emphasize the importance of protein phosphorylation in the regulation of cellular processes in the Archaea.

  • 161.
    Reischauer, Sven
    et al.
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Max Planck Inst Heart & Lung Res, Dept Dev Genet, D-61231 Bad Nauheim, Germany..
    Stone, Oliver A.
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Max Planck Inst Heart & Lung Res, Dept Dev Genet, D-61231 Bad Nauheim, Germany..
    Villasenor, Alethia
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Max Planck Inst Heart & Lung Res, Dept Dev Genet, D-61231 Bad Nauheim, Germany..
    Chi, Neil
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Univ Calif San Diego, Inst Genom Med, Div Cardiol, Dept Med, La Jolla, CA 92037 USA..
    Jin, Suk-Won
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Gwangju Inst Sci & Technol, Sch Life Sci, Gwangju 61005, South Korea.;Yale Univ, Sch Med, Yale Cardiovasc Res Ctr, New Haven, CT 06511 USA..
    Martin, Marcel
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, S-17121 Solna, Sweden..
    Lee, Miler T.
    Yale Univ, Dept Genet, Sch Med, New Haven, CT 06520 USA.;Univ Pittsburgh, Dept Biol Sci, Pittsburgh, PA 15260 USA..
    Fukuda, Nana
    Max Planck Inst Heart & Lung Res, Dept Dev Genet, D-61231 Bad Nauheim, Germany..
    Marass, Michele
    Max Planck Inst Heart & Lung Res, Dept Dev Genet, D-61231 Bad Nauheim, Germany..
    Witty, Alec
    Univ Calif San Diego, Inst Genom Med, Div Cardiol, Dept Med, La Jolla, CA 92037 USA..
    Fiddes, Ian
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Univ Calif Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA.;Howard Hughes Med Inst, Santa Cruz, CA 95064 USA..
    Kuo, Taiyi
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Columbia Univ Coll Phys & Surg, Dept Med, 630 W 168th St, New York, NY 10032 USA.;Columbia Univ Coll Phys & Surg, Berrie Diabet Ctr, 630 W 168th St, New York, NY 10032 USA..
    Chung, Won-Suk
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Korea Adv Inst Sci & Technol, Dept Biol Sci, Daejeon 34141, South Korea..
    Salek, Sherveen
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Johns Hopkins Univ Hosp, Wilmer Eye Inst, Baltimore, MD 21224 USA..
    Lerrigo, Robert
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Univ Washington, Div Gen Internal Med, Seattle, WA 98104 USA..
    Alsio, Jessica
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Novartis, CH-4056 Basel, Switzerland..
    Luo, Shujun
    Illumina, San Diego, CA 92122 USA.;Personalis, Menlo Pk, CA 94025 USA..
    Tworus, Dominika
    Karolinska Inst, Dept Cell & Mol Biol, S-17177 Stockholm, Sweden..
    Augustine, Sruthy M.
    Max Planck Inst Heart & Lung Res, Dept Dev Genet, D-61231 Bad Nauheim, Germany..
    Mucenieks, Sophie
    Max Planck Inst Heart & Lung Res, Dept Dev Genet, D-61231 Bad Nauheim, Germany..
    Nystedt, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Giraldez, Antonio J.
    Yale Univ, Dept Genet, Sch Med, New Haven, CT 06520 USA..
    Schroth, Gary P.
    Illumina, San Diego, CA 92122 USA..
    Andersson, Olov
    Karolinska Inst, Dept Cell & Mol Biol, S-17177 Stockholm, Sweden..
    Stainier, Didier Y. R.
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.;Max Planck Inst Heart & Lung Res, Dept Dev Genet, D-61231 Bad Nauheim, Germany..
    Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 535, no 7611, p. 294-+Article in journal (Refereed)
    Abstract [en]

    Vascular and haematopoietic cells organize into specialized tissues during early embryogenesis to supply essential nutrients to all organs and thus play critical roles in development and disease. At the top of the haemato-vascular specification cascade lies cloche, a gene that when mutated in zebrafish leads to the striking phenotype of loss of most endothelial and haematopoietic cells(1-4) and a significant increase in cardiomyocyte numbers(5). Although this mutant has been analysed extensively to investigate mesoderm diversification and differentiation(1-7) and continues to be broadly used as a unique avascular model, the isolation of the cloche gene has been challenging due to its telomeric location. Here we used a deletion allele of cloche to identify several new cloche candidate genes within this genomic region, and systematically genome-edited each candidate. Through this comprehensive interrogation, we succeeded in isolating the cloche gene and discovered that it encodes a PAS-domain-containing bHLH transcription factor, and that it is expressed in a highly specific spatiotemporal pattern starting during late gastrulation. Gain-of-function experiments show that it can potently induce endothelial gene expression. Epistasis experiments reveal that it functions upstream of etv2 and tal1, the earliest expressed endothelial and haematopoietic transcription factor genes identified to date. A mammalian cloche orthologue can also rescue blood vessel formation in zebrafish cloche mutants, indicating a highly conserved role in vertebrate vasculogenesis and haematopoiesis. The identification of this master regulator of endothelial and haematopoietic fate enhances our understanding of early mesoderm diversification and may lead to improved protocols for the generation of endothelial and haematopoietic cells in vivo and in vitro.

  • 162. Richards, Stephen
    et al.
    Gibbs, Richard A.
    Gerardo, Nicole M.
    Moran, Nancy
    Nakabachi, Atsushi
    Stern, David
    Tagu, Denis
    Wilson, Alex C. C.
    Muzny, Donna
    Kovar, Christie
    Cree, Andy
    Chacko, Joseph
    Chandrabose, Mimi N.
    Dao, Marvin Diep
    Dinh, Huyen H.
    Gabisi, Ramatu Ayiesha
    Hines, Sandra
    Hume, Jennifer
    Jhangian, Shalini N.
    Joshi, Vandita
    Lewis, Lora R.
    Liu, Yih-shin
    Lopez, John
    Morgan, Margaret B.
    Nguyen, Ngoc Bich
    Okwuonu, Geoffrey O.
    Ruiz, San Juana
    Santibanez, Jireh
    Wright, Rita A.
    Fowler, Gerald R.
    Hitchens, Matthew E.
    Lozado, Ryan J.
    Moen, Charles
    Steffen, David
    Warren, James T.
    Zhang, Jingkun
    Nazareth, Lynne V.
    Chavez, Dean
    Davis, Clay
    Lee, Sandra L.
    Patel, Bella Mayurkumar
    Pu, Ling-Ling
    Bell, Stephanie N.
    Johnson, Angela Jolivet
    Vattathil, Selina
    Williams, Rex L., Jr.
    Shigenobu, Shuji
    Dang, Phat M.
    Morioka, Mizue
    Fukatsu, Takema
    Kudo, Toshiaki
    Miyagishima, Shin-ya
    Jiang, Huaiyang
    Worley, Kim C.
    Legeai, Fabrice
    Gauthier, Jean-Pierre
    Collin, Olivier
    Zhang, Lan
    Chen, Hsiu-Chuan
    Ermolaeva, Olga
    Hlavina, Wratko
    Kapustin, Yuri
    Kiryutin, Boris
    Kitts, Paul
    Maglott, Donna
    Murphy, Terence
    Pruitt, Kim
    Sapojnikov, Victor
    Souvorov, Alexandre
    Thibaud-Nissen, Francoise
    Camara, Francisco
    Guigo, Roderic
    Stanke, Mario
    Solovyev, Victor
    Kosarev, Peter
    Gilbert, Don
    Gabaldon, Toni
    Huerta-Cepas, Jaime
    Marcet-Houben, Marina
    Pignatelli, Miguel
    Moya, Andres
    Rispe, Claude
    Ollivier, Morgane
    Quesneville, Hadi
    Permal, Emmanuelle
    Llorens, Carlos
    Futami, Ricardo
    Hedges, Dale
    Robertson, Hugh M.
    Alioto, Tyler
    Mariotti, Marco
    Nikoh, Naruo
    McCutcheon, John P.
    Burke, Gaelen
    Kamins, Alexandra
    Latorre, Amparo
    Moran, Nancy A.
    Ashton, Peter
    Calevro, Federica
    Charles, Hubert
    Colella, Stefano
    Douglas, Angela
    Jander, Georg
    Jones, Derek H.
    Febvay, Gerard
    Kamphuis, Lars G.
    Kushlan, Philip F.
    Macdonald, Sandy
    Ramsey, John
    Schwartz, Julia
    Seah, Stuart
    Thomas, Gavin
    Vellozo, Augusto
    Cass, Bodil
    Degnan, Patrick
    Hurwitz, Bonnie
    Leonardo, Teresa
    Koga, Ryuichi
    Altincicek, Boran
    Anselme, Caroline
    Atamian, Hagop
    Barribeau, Seth M.
    de Vos, Martin
    Duncan, Elizabeth J.
    Evans, Jay
    Ghanim, Murad
    Heddi, Abdelaziz
    Kaloshian, Isgouhi
    Vincent-Monegat, Carole
    Parker, Ben J.
    Perez-Brocal, Vicente
    Rahbe, Yvan
    Spragg, Chelsea J.
    Tamames, Javier
    Tamarit, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Tamborindeguy, Cecilia
    Vilcinskas, Andreas
    Bickel, Ryan D.
    Brisson, Jennifer A.
    Butts, Thomas
    Chang, Chun-che
    Christiaens, Olivier
    Davis, Gregory K.
    Duncan, Elizabeth
    Ferrier, David
    Iga, Masatoshi
    Janssen, Ralf
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Lu, Hsiao-Ling
    McGregor, Alistair
    Miura, Toru
    Smagghe, Guy
    Smith, James
    van der Zee, Maurijn
    Velarde, Rodrigo
    Wilson, Megan
    Dearden, Peter
    Edwards, Owain R.
    Gordon, Karl
    Hilgarth, Roland S.
    Rider, Stanley Dean, Jr.
    Srinivasan, Dayalan
    Walsh, Thomas K.
    Ishikawa, Asano
    Jaubert-Possamai, Stephanie
    Fenton, Brian
    Huang, Wenting
    Rizk, Guillaume
    Lavenier, Dominique
    Nicolas, Jacques
    Smadja, Carole
    Zhou, Jing-Jiang
    Vieira, Filipe G.
    He, Xiao-Li
    Liu, Renhu
    Rozas, Julio
    Field, Linda M.
    Ashton, Peter D.
    Campbell, Peter
    Carolan, James C.
    Douglas, Angela E.
    Fitzroy, Carol I. J.
    Reardon, Karen T.
    Reeck, Gerald R.
    Singh, Karam
    Wilkinson, Thomas L.
    Huybrechts, Jurgen
    Abdel-latief, Mohatmed
    Robichon, Alain
    Veenstra, Jan A.
    Hauser, Frank
    Cazzamali, Giuseppe
    Schneider, Martina
    Williamson, Michael
    Stafflinger, Elisabeth
    Hansen, Karina K.
    Grimmelikhuijzen, Cornelis J. P.
    Price, Daniel R. G.
    Caillaud, Marina
    van Fleet, Eric
    Ren, Qinghu
    Gatehouse, John A.
    Brault, Veronique
    Monsion, Baptiste
    Diaz, Jason
    Hunnicutt, Laura
    Ju, Ho-Jong
    Pechuan, Ximo
    Aguilar, Jose
    Cortes, Teresa
    Ortiz-Rivas, Benjamin
    Martinez-Torres, David
    Dombrovsky, Aviv
    Dale, Richard P.
    Davies, T. G. Emyr
    Williamson, Martin S.
    Jones, Andrew
    Sattelle, David
    Williamson, Sally
    Wolstenholme, Adrian
    Cottret, Ludovic
    Sagot, Marie France
    Heckel, David G.
    Hunter, Wayne
    Genome Sequence of the Pea Aphid Acyrthosiphon pisum2010In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 8, no 2, p. e1000313-Article in journal (Refereed)
    Abstract [en]

    Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

  • 163.
    Riess, Kai
    et al.
    Univ Koblenz Landau, Inst Environm Sci, Ecosyst Anal, Fortstr 7, D-76829 Landau, Germany.
    Schön, Max Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Tubingen, Inst Evolut & Ecol, Plant Evolutionary Ecol, Morgenstelle 5, D-72076 Tubingen, Germany.
    Ziegler, Rebekka
    Univ Tubingen, Inst Evolut & Ecol, Plant Evolutionary Ecol, Morgenstelle 5, D-72076 Tubingen, Germany.
    Lutz, Matthias
    Univ Tubingen, Inst Evolut & Ecol, Plant Evolutionary Ecol, Morgenstelle 5, D-72076 Tubingen, Germany.
    Shivas, Roger G.
    Univ Southern Queensland, Ctr Crop Hlth, Inst Agr & Environm, Toowoomba, Qld 4350, Australia.
    Piatek, Marcin
    Polish Acad Sci, W Szafer Inst Bot, Dept Mycol, Lubicz 46, PL-31512 Krakow, Poland.
    Garnica, Sigisfredo
    Univ Tubingen, Inst Evolut & Ecol, Plant Evolutionary Ecol, Morgenstelle 5, D-72076 Tubingen, Germany;Univ Austral Chile, Inst Bioquim & Microbiol, Casilla 567, Valdivia, Chile.
    The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae2019In: Organisms Diversity & Evolution, ISSN 1439-6092, E-ISSN 1618-1077, Vol. 19, no 1, p. 13-30Article in journal (Refereed)
    Abstract [en]

    Fungi belonging to the Entorrhizales (Entorrhizomycota) comprise biotrophic pathogens associated with roots of theCyperaceae and Juncaceae plant species. They are nearly globally distributed but rarely studied due to a hidden lifestyle without causing visible effects on host plants. Therefore, the evolutionary origin and phylogenetic relationships of the group are still poorly understood and it is not known whether species diversification was the result of co-evolution with their hosts or the result of host jumps. To infer hypotheses about the evolutionary history of the Entorrhizales, divergence times were estimated and plant-fungal tanglegrams calculated. Relaxed molecular clock analyses suggest that the Entorrhizomycota originated around the Neoproterozoic-Palaeozoic and diverged during the Late Cretaceous-Paleogene into the extant orders Entorrhizales and Talbotiomycetales. The split of the major lineages within the Entorrhizales took place in the Eocene, somewhat later than the divergence of the host families Cyperaceae and Juncaceae. Topology- and distance-based co-phylogenetic analyses of the fungi and their hosts revealed a large number of co-speciation and lineage sorting events in early fungal speciation, which resulted in a phylogenetic split corresponding to species infecting Cyperaceae or Juncaceae. Given that this split is congruent with spore differences, Entorrhiza s. str. is emended for species infecting hosts in the Cyperaceae, and a new genus Juncorrhiza is described for species restricted to hosts in the Juncaceae. Additionally, three new species are described: Entorrhiza fuirenae, Juncorrhiza maritima and J. oxycarpi.

  • 164.
    Roxström-Lindquist, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Jerlström-Hultqvist, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Jörgensen, Anders
    Troell, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Svärd, Staffan G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Andersson, Jan O.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Molecular Evolution.
    Large genomic differences between the morphologically indistinguishable diplomonads Spironucleus barkhanus and Spironucleus salmonicida.2010In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, p. 258-Article in journal (Refereed)
    Abstract [en]

    Background

    Microbial eukaryotes show large variations in genome structure and content between lineages, indicating extensive flexibility over evolutionary timescales. Here we address the tempo and mode of such changes within diplomonads, flagellated protists with two nuclei found in oxygen-poor environments. Approximately 5,000 expressed sequence tag (EST) sequences were generated from the fish commensal Spironucleus barkhanus and compared to sequences from the morphologically indistinguishable fish parasite Spironucleus salmonicida, and other diplomonads. The ESTs were complemented with sequence variation studies in selected genes and genome size determinations.

    Results

    Many genes detected in S. barkhanus and S. salmonicida are absent in the human parasite Giardia intestinalis, the most intensively studied diplomonad. For example, these fish diplomonads show an extended metabolic repertoire and are able to incorporate selenocysteine into proteins. The codon usage is altered in S. barkhanus compared to S. salmonicida. Sequence variations were found between individual S. barkhanus ESTs for many, but not all, protein coding genes. Conversely, no allelic variation was found in a previous genome survey of S. salmonicida. This difference was confirmed by sequencing of genomic DNA. Up to five alleles were identified for the cloned S. barkhanus genes, and at least nineteen highly expressed S. barkhanus genes are represented by more than four alleles in the EST dataset. This could be explained by the presence of a non-clonal S. barkhanus population in the culture, by a ploidy above four, or by duplications of parts of the genome. Indeed, genome size estimations using flow cytometry indicated similar haploid genome sizes in S. salmonicida and G. intestinalis (similar to 12 Mb), whereas the S. barkhanus genome is larger (similar to 18 Mb).

    Conclusions

    This study indicates extensive divergent genome evolution within diplomonads. Genomic traits such as codon usage, frequency of allelic sequence variation, and genome size have changed considerably between S. barkhanus and S. salmonicida. These observations suggest that large genomic differences may accumulate in morphologically indistinguishable eukaryotic microbes.

  • 165.
    Saenko, Suzanne V.
    et al.
    Univ Geneva, Dept Genet & Evolut, LANE, CH-1211 Geneva 4, Switzerland..
    Lamichhaney, Sangeet
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Barrio, Alvaro Martinez
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Rafati, Nima
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.;Texas A&M Univ, Coll Vet Med & Biomed Sci, Dept Vet Integrat Biosci, College Stn, TX USA..
    Milinkovitch, Michel C.
    Univ Geneva, Dept Genet & Evolut, LANE, CH-1211 Geneva 4, Switzerland.;SIB Swiss Inst Bioinformat, Geneva, Switzerland..
    Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 17118Article in journal (Refereed)
    Abstract [en]

    The corn snake (Pantherophis guttatus) is a new model species particularly appropriate for investigating the processes generating colours in reptiles because numerous colour and pattern mutants have been isolated in the last five decades. Using our captive-bred colony of corn snakes, transcriptomic and genomic next-generation sequencing, exome assembly, and genotyping of SNPs in multiple families, we delimit the genomic interval bearing the causal mutation of amelanism, the oldest colour variant observed in that species. Proceeding with sequencing the candidate gene OCA2 in the uncovered genomic interval, we identify that the insertion of an LTR-retrotransposon in its 11th intron results in a considerable truncation of the p protein and likely constitutes the causal mutation of amelanism in corn snakes. As amelanistic snakes exhibit white, instead of black, borders around an otherwise normal pattern of dorsal orange saddles and lateral blotches, our results indicate that melanocytes lacking melanin are able to participate to the normal patterning of other colours in the skin. In combination with research in the zebrafish, this work opens the perspective of using corn snake colour and pattern variants to investigate the generative processes of skin colour patterning shared among major vertebrate lineages.

  • 166. Saha, Indrajit
    et al.
    Zubek, Julian
    Klingstrom, Tomas
    Forsberg, Simon
    Wikander, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Kierczak, Marcin
    Maulik, Ujjwal
    Plewczynski, Dariusz
    Ensemble learning prediction of protein-protein interactions using proteins functional annotations2014In: MOL BIOSYST, ISSN 1742-206X, Vol. 10, no 4, p. 820-830Article in journal (Refereed)
    Abstract [en]

    Protein-protein interactions are important for the majority of biological processes. A significant number of computational methods have been developed to predict protein-protein interactions using protein sequence, structural and genomic data. Vast experimental data is publicly available on the Internet, but it is scattered across numerous databases. This fact motivated us to create and evaluate new high-throughput datasets of interacting proteins. We extracted interaction data from DIP, MINT, BioGRID and IntAct databases. Then we constructed descriptive features for machine learning purposes based on data from Gene Ontology and DOMINE. Thereafter, four well-established machine learning methods: Support Vector Machine, Random Forest, Decision Tree and Naive Bayes, were used on these datasets to build an Ensemble Learning method based on majority voting. In cross-validation experiment, sensitivity exceeded 80% and classification/prediction accuracy reached 90% for the Ensemble Learning method. We extended the experiment to a bigger and more realistic dataset maintaining sensitivity over 70%. These results confirmed that our datasets are suitable for performing PPI prediction and Ensemble Learning method is well suited for this task. Both the processed PPI datasets and the software are available at http://sysbio.icm.edu.pl/indra/EL-PPI/home.html.

  • 167.
    Saw, Jimmy H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zaremba-Niedzwiedzka, Katarzyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Juzokaite, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala Univ, Dept Cell & Mol Biol, Sci Life Lab, Uppsala, Sweden..
    Dodsworth, Jeremy A.
    Univ Nevada, Sch Life Sci, Las Vegas, NV 89154 USA..
    Murugapiran, Senthil K.
    Univ Nevada, Sch Life Sci, Las Vegas, NV 89154 USA..
    Colman, Dan R.
    Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USA..
    Takacs-Vesbach, Cristina
    Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USA..
    Hedlund, Brian P.
    Univ Nevada, Sch Life Sci, Las Vegas, NV 89154 USA..
    Guy, Lionel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes2015In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 370, no 1678, article id 20140328Article in journal (Refereed)
    Abstract [en]

    The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteo-bacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal 'dark matter', is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.

  • 168. Schneider, Daniela I.
    et al.
    Klasson, Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Lind, Anders E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Miller, Wolfgang J.
    More than fishing in the dark: PCR of a dispersed sequence produces simple but ultrasensitive Wolbachia detection2014In: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 14, p. 121-Article in journal (Refereed)
    Abstract [en]

    Background: Detecting intracellular bacterial symbionts can be challenging when they persist at very low densities. Wolbachia, a widespread bacterial endosymbiont of invertebrates, is particularly challenging. Although it persists at high titers in many species, in others its densities are far below the detection limit of classic end-point Polymerase Chain Reaction (PCR). These low-titer infections can be reliably detected by combining PCR with DNA hybridization, but less elaborate strategies based on end-point PCR alone have proven less sensitive or less general. Results: We introduce a multicopy PCR target that allows fast and reliable detection of A-supergroup Wolbachia -even at low infection titers -with standard end-point PCR. The target is a multicopy motif (designated ARM: A-supergroup repeat motif) discovered in the genome of wMel (the Wolbachia in Drosophila melanogaster). ARM is found in at least seven other Wolbachia A-supergroup strains infecting various Drosophila, the wasp Muscidifurax and the tsetse fly Glossina. We demonstrate that end-point PCR targeting ARM can reliably detect both high-and low-titer Wolbachia infections in Drosophila, Glossina and interspecific hybrids. Conclusions: Simple end-point PCR of ARM facilitates detection of low-titer Wolbachia A-supergroup infections. Detecting these infections previously required more elaborate procedures. Our ARM target seems to be a general feature of Wolbachia A-supergroup genomes, unlike other multicopy markers such as insertion sequences (IS).

  • 169.
    Schulz, Frederik
    et al.
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Althanstr 14, Vienna, Austria..
    Martijn, Joran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wascher, Florian
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Althanstr 14, Vienna, Austria..
    Lagkouvardos, Ilias
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Althanstr 14, Vienna, Austria..
    Kostanjsek, Rok
    Univ Ljubljana, Dept Biol, Vecna Pot 111, Ljubljana, Slovenia..
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Horn, Matthias
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Althanstr 14, Vienna, Austria..
    A Rickettsiales symbiont of amoebae with ancient features2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 8, p. 2326-2342Article in journal (Refereed)
    Abstract [en]

    The Rickettsiae comprise intracellular bacterial symbionts and pathogens infecting diverse eukaryotes. Here, we provide a detailed characterization of CandidatusJidaibacter acanthamoeba', a rickettsial symbiont of Acanthamoeba. The bacterium establishes the infection in its amoeba host within 2h where it replicates within vacuoles. Higher bacterial loads and accelerated spread of infection at elevated temperatures were observed. The infection had a negative impact on host growth rate, although no increased levels of host cell lysis were seen. Phylogenomic analysis identified this bacterium as member of the Midichloriaceae. Its 2.4Mb genome represents the largest among Rickettsiales and is characterized by a moderate degree of pseudogenization and a high coding density. We found an unusually large number of genes encoding proteins with eukaryotic-like domains such as ankyrins, leucine-rich repeats and tetratricopeptide repeats, which likely function in host interaction. There are a total of three divergent, independently acquired type IV secretion systems, and 35 flagellar genes representing the most complete set found in an obligate intracellular Alphaproteobacterium. The deeply branching phylogenetic position of CandidatusJidaibacter acanthamoeba' together with its ancient features place it closely to the rickettsial ancestor and helps to better understand the transition from a free-living to an intracellular lifestyle.

  • 170.
    Schwank, Katrin
    et al.
    Univ Duisburg Essen, Biofilm Ctr, Dept Chem, GAME, Duisburg, Germany.
    Bornemann, Till L., V
    Univ Duisburg Essen, Biofilm Ctr, Dept Chem, GAME, Duisburg, Germany.
    Dombrowski, Nina
    Univ Utrecht, Royal Netherlands Inst Sea Res NIOZ, Dept Marine Microbiol & Biogeochem MMB, Den Burg, Netherlands.
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Utrecht, Royal Netherlands Inst Sea Res NIOZ, Dept Marine Microbiol & Biogeochem MMB, Den Burg, Netherlands.
    Banfield, Jillian F.
    Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA.
    Probst, Alexander J.
    Univ Duisburg Essen, Biofilm Ctr, Dept Chem, GAME, Duisburg, Germany.
    An archaeal symbiont-host association from the deep terrestrial subsurface2019In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 13, no 8, p. 2135-2139Article in journal (Refereed)
    Abstract [en]

    DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal hostsymbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.

  • 171.
    Seeger, Christian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Butler, Margaret K.
    Univ Queensland, Sch Chem & Mol Biosci, Australian Ctr Ecogen, Brisbane, Qld 4072, Australia..
    Yee, Benjamin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Mahajan, Mayank
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Fuerst, John A.
    Univ Queensland, Sch Chem & Mol Biosci, Brisbane, Qld 4072, Australia..
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Tuwongella immobilis gen. nov., sp nov., a novel non-motile bacterium within the phylum Planctomycetes2017In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 67, no 12, p. 4923-4929Article in journal (Refereed)
    Abstract [en]

    A gram-negative, budding, catalase negative, oxidase positive and non-motile bacterium (MBLW1(T)) with a complex endomembrane system has been isolated from a freshwater lake in southeast Queensland, Australia. Phylogeny based on 16S rRNA gene sequence analysis places the strain within the family Planctomycetaceae, related to Zavarzinella formosa (93.3 %), Telmatocola sphagniphila (93.3 %) and Gemmata obscuriglobus (91.9 %). Phenotypic and chemotaxonomic analysis demonstrates considerable differences to the type strains of the related genera. MBLW1(T) displays modest salt tolerance and grows optimally at pH values of 7.5-8.0 and at temperatures of 32-36 degrees C. Transmission electron microscopy analysis demonstrates the presence of a complex endomembrane system, however, without the typically condensed nucleoid structure found in related genera. The major fatty acids are 16 : 1 omega 5c, 16 : 0 and 18 : 0. Based on discriminatory results from 16S rRNA gene sequence analysis, phenotypic, biochemical and chemotaxonomic analysis, MBLW1(T) should be considered as a new genus and species, for which the name Tuwongella immobilis gen. nov., sp. nov. is proposed. The type strain is MBLW1(T) (=CCUG 69661(T) =DSM 105045(T)).

  • 172.
    Seitz, Kiley W.
    et al.
    Univ Texas Austin, Dept Marine Sci, Port Aransas, TX 78373 USA.
    Dombrowski, Nina
    Univ Texas Austin, Dept Marine Sci, Port Aransas, TX 78373 USA;Royal Netherlands Inst Sea Res, NIOZ, NL-1797 SZ Den Burg, Netherlands;Univ Utrecht, NL-1797 SZ Den Burg, Netherlands.
    Eme, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Paris Sud, Unite Ecol Systemat & Evolut, CNRS, F-91400 Orsay, France.
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Royal Netherlands Inst Sea Res, NIOZ, NL-1797 SZ Den Burg, Netherlands;Univ Utrecht, NL-1797 SZ Den Burg, Netherlands.
    Lombard, Jonathan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sieber, Jessica R.
    Univ Minnesota, Duluth, MN 55812 USA.
    Teske, Andreas P.
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Wageningen Univ, Dept Agrotechnol & Food Sci, Lab Microbiol, NL-6708 WE Wageningen, Netherlands.
    Baker, Brett J.
    Univ Texas Austin, Dept Marine Sci, Port Aransas, TX 78373 USA.
    Asgard archaea capable of anaerobic hydrocarbon cycling2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 1822Article in journal (Refereed)
    Abstract [en]

    Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.

  • 173. Sentchilo, Vladimir
    et al.
    Mayer, Antonia P.
    Guy, Lionel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Miyazaki, Ryo
    Tringe, Susannah Green
    Barry, Kerrie
    Malfatti, Stephanie
    Goessmann, Alexander
    Robinson-Rechavi, Marc
    van der Meer, Jan R.
    Community-wide plasmid gene mobilization and selection2013In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, no 6, p. 1173-1186Article in journal (Refereed)
    Abstract [en]

    Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host's chromosome and their frequent self-transfer. It is thought that plasmids accumulate, rearrange and distribute nonessential genes, which may provide an advantage for host proliferation under selective conditions. In order to test this hypothesis independently of biases from culture selection, we study the plasmid metagenome from microbial communities in two activated sludge systems, one of which receives mostly household and the other chemical industry wastewater. We find that plasmids from activated sludge microbial communities carry among the largest proportion of unknown gene pools so far detected in metagenomic DNA, confirming their presumed role of DNA innovators. At a system level both plasmid metagenomes were dominated by functions associated with replication and transposition, and contained a wide variety of antibiotic and heavy metal resistances. Plasmid families were very different in the two metagenomes and grouped in deep-branching new families compared with known plasmid replicons. A number of abundant plasmid replicons could be completely assembled directly from the metagenome, providing insight in plasmid composition without culturing bias. Functionally, the two metagenomes strongly differed in several ways, including a greater abundance of genes for carbohydrate metabolism in the industrial and of general defense factors in the household activated sludge plasmid metagenome. This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions.

  • 174.
    Shebanits, Kateryna
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Larhammar: Pharmacology.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Johansson, Anna C. V.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Maqbool, Khurram
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Feuk, Lars
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Larhammar, Dan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Larhammar: Pharmacology.
    Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.2019In: BMC Biotechnology, ISSN 1472-6750, E-ISSN 1472-6750, Vol. 19, article id 31Article in journal (Refereed)
    Abstract [en]

    Background: Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene for the appetite-regulating pancreatic polypeptide receptor Y4. This genomic region has been challenging to map due to multiple repeated elements and its precise organization has not yet been resolved. Previous studies using microarrays were interpreted to show that the most common copy number was 2 per genome.

    Results: We have investigated 18 individuals from the 1000 Genomes project using the well-established method of read depth analysis and the new droplet digital PCR (ddPCR) method. We find that the most common copy number for NPY4R is 4. The estimated number of copies ranged from three to seven based on read depth analyses with Control-FREEC and CNVnator, and from four to seven based on ddPCR. We suggest that the difference between our results and those published previously can be explained by methodological differences such as reference gene choice, data normalization and method reliability. Three high-quality archaic human genomes (two Neanderthal and one Denisova) display four copies of the NPY4R gene indicating that a duplication occurred prior to the human-Neanderthal/Denisova split.

    Conclusions: We conclude that ddPCR is a sensitive and reliable method for CNV determination, that it can be used for read depth calibration in CNV studies based on already available whole-genome sequencing data, and that further investigation of NPY4R copy number variation and its consequences are necessary due to the role of Y4 receptor in food intake regulation.

  • 175. Siozios, Stefanos
    et al.
    Ioannidis, Panagiotis
    Klasson, Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Braig, Henk R.
    Bourtzis, Kostas
    The Diversity and Evolution of Wolbachia Ankyrin Repeat Domain Genes2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 2, p. e55390-Article in journal (Refereed)
    Abstract [en]

    Ankyrin repeat domain-encoding genes are common in the eukaryotic and viral domains of life, but they are rare in bacteria, the exception being a few obligate or facultative intracellular Proteobacteria species. Despite having a reduced genome, the arthropod strains of the alphaproteobacterium Wolbachia contain an unusually high number of ankyrin repeat domain-encoding genes ranging from 23 in wMel to 60 in wPip strain. This group of genes has attracted considerable attention for their astonishing large number as well as for the fact that ankyrin proteins are known to participate in protein-protein interactions, suggesting that they play a critical role in the molecular mechanism that determines host-Wolbachia symbiotic interactions. We present a comparative evolutionary analysis of the wMel-related ankyrin repeat domain-encoding genes present in different Drosophila-Wolbachia associations. Our results show that the ankyrin repeat domain-encoding genes change in size by expansion and contraction mediated by short directly repeated sequences. We provide examples of intragenic recombination events and show that these genes are likely to be horizontally transferred between strains with the aid of bacteriophages. These results confirm previous findings that the Wolbachia genomes are evolutionary mosaics and illustrate the potential that these bacteria have to generate diversity in proteins potentially involved in the symbiotic interactions.

  • 176.
    Spang, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Caceres, Eva F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life.2017In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 357, no 6351, article id eaaf3883Article, review/survey (Refereed)
    Abstract [en]

    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.

  • 177.
    Spang, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, NIOZ, Den Burg, Netherlands.; Univ Utrecht, Den Burg, Netherlands.
    Eme, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Saw, Jimmy H.
    Oregon State Univ, Dept Microbiol, Corvallis, OR USA.
    Fernández Cáceres, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zaremba-Niedzwiedzka, Katarzyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lombard, Jonathan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Guy, Lionel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Asgard archaea are the closest prokaryotic relatives of eukaryotes2018In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 14, no 3, article id e1007080Article in journal (Other academic)
  • 178.
    Spang, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Archaeal evolution: The methanogenic roots of Archaea2017In: Nature Microbiology, E-ISSN 2058-5276, Vol. 2, article id 17109Article in journal (Other academic)
  • 179.
    Spang, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Microbial Diversity: The tree of life comes of age2016In: Nature Microbiology, E-ISSN 2058-5276, Vol. 1, no 5, article id 16056Article in journal (Other (popular science, discussion, etc.))
  • 180.
    Spang, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Martijn, Joran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Saw, Jimmy Hser Wah
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lind, Anders E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Guy, Lionel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution2013In: Archaea, ISSN 1472-3646, E-ISSN 1472-3654, Vol. 2013, p. 202358-Article, review/survey (Refereed)
    Abstract [en]

    The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life.

  • 181.
    Spang, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Royal Netherlands Inst Sea Res, NIOZ, Dept Marine Microbiol & Biogeochem, NL-1790 AB Den Burg, Netherlands;Univ Utrecht, NL-1790 AB Den Burg, Netherlands.
    Offre, Pierre
    Royal Netherlands Inst Sea Res, NIOZ, Dept Marine Microbiol & Biogeochem, NL-1790 AB Den Burg, Netherlands;Univ Utrecht, NL-1790 AB Den Burg, Netherlands.
    Towards a systematic understanding of differences between archaeal and bacterial diversity2019In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 11, no 1, p. 9-12Article in journal (Refereed)
    Abstract [en]

    In this crystal ball, we discuss emerging methodologies that can help reaching a synthesis on the biodiversity of Archaea and Bacteria and thereby inform a central enigma in microbiology, i.e. the fundamental split between these primary domains of life and the apparent lower diversity of the Archaea.

  • 182.
    Spang, Anja
    et al.