LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 136

Search options

  1. Article ; Online: Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota.

    Odelgard, Anna / Hägglund, Emil / Guy, Lionel / Andersson, Siv G E

    Genome biology and evolution

    2024  Volume 16, Issue 4

    Abstract: The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally ...

    Abstract The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca. Uabimicrobium amorphum", of which 66 families contained eukaryotic-like Serine/Threonine kinases with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases in "Ca. Uabimicrobium amorphum". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.
    MeSH term(s) Protein Serine-Threonine Kinases/genetics ; Protein Serine-Threonine Kinases/metabolism ; Phylogeny ; Planctomycetes ; Proteome/genetics ; Bacteria/genetics ; Bacteria/metabolism ; Threonine/genetics ; Serine/genetics
    Chemical Substances Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Proteome ; Threonine (2ZD004190S) ; Serine (452VLY9402)
    Language English
    Publishing date 2024-03-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 2495328-3
    ISSN 1759-6653 ; 1759-6653
    ISSN (online) 1759-6653
    ISSN 1759-6653
    DOI 10.1093/gbe/evae068
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article ; Online: TADA: taxonomy-aware dataset aggregator.

    Hägglund, Emil / Andersson, Siv G E / Guy, Lionel

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 12

    Abstract: Summary: The profusion of sequenced genomes across the bacterial and archeal domains offers unprecedented possibilities for phylogenetic and comparative genomic analyses. In general, phylogenetic reconstruction is improved by the use of more data. ... ...

    Abstract Summary: The profusion of sequenced genomes across the bacterial and archeal domains offers unprecedented possibilities for phylogenetic and comparative genomic analyses. In general, phylogenetic reconstruction is improved by the use of more data. However, including all available data is (i) not computationally tractable, and (ii) prone to biases, as the abundance of genomes is very unequally distributed over the biological diversity. Thus, in most cases, subsampling taxa to build a phylogeny is necessary. Currently, though, there is no available software to perform that handily. Here we present TADA, a taxonomic-aware dataset selection workflow that allows sampling across user-defined portions of the prokaryotic diversity with variable granularity, while setting constraints on genome quality and balance between branches.
    Availability and implementation: TADA is implemented as a snakemake workflow and is freely available at https://github.com/emilhaegglund/TADA.
    MeSH term(s) Phylogeny ; Software ; Genome ; Bacteria/genetics ; Archaea/genetics
    Language English
    Publishing date 2023-12-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad742
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: Apilactobacillus kunkeei

    Seeger, Christian / Dyrhage, Karl / Näslund, Kristina / Andersson, Siv G E

    microLife

    2023  Volume 4, Page(s) uqad037

    Abstract: Extracellularly released particles, including membrane vesicles, have increasingly been recognized as important for bacterial community functions and host-interaction processes, but their compositions and functional roles differ between species and also ... ...

    Abstract Extracellularly released particles, including membrane vesicles, have increasingly been recognized as important for bacterial community functions and host-interaction processes, but their compositions and functional roles differ between species and also between strains of the same species. In this study, we have determined the composition of membrane vesicles and protein particles identified in the cell-free pellets of two strains of
    Language English
    Publishing date 2023-08-29
    Publishing country England
    Document type Journal Article
    ISSN 2633-6693
    ISSN (online) 2633-6693
    DOI 10.1093/femsml/uqad037
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Rethinking microbial symbioses.

    Tamarit, Daniel / Andersson, Siv G E

    FEMS microbiology letters

    2020  Volume 367, Issue 3

    MeSH term(s) Archaea/physiology ; Bacterial Physiological Phenomena ; Host Microbial Interactions ; Research/trends ; Symbiosis
    Language English
    Publishing date 2020-03-19
    Publishing country England
    Document type Editorial ; Research Support, Non-U.S. Gov't
    ZDB-ID 752343-9
    ISSN 1574-6968 ; 0378-1097
    ISSN (online) 1574-6968
    ISSN 0378-1097
    DOI 10.1093/femsle/fnz255
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 1372: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article ; Online: Stress management strategies in single bacterial cells.

    Andersson, Siv G E

    Proceedings of the National Academy of Sciences of the United States of America

    2016  Volume 113, Issue 15, Page(s) 3921–3923

    MeSH term(s) Humans ; Stress, Psychological ; Surveys and Questionnaires
    Language English
    Publishing date 2016-04-12
    Publishing country United States
    Document type Editorial ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1603151113
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Article ; Online: Folded Alpha Helical Putative New Proteins from Apilactobacillus kunkeei.

    Ye, Weihua / Krishna Behra, Phani Rama / Dyrhage, Karl / Seeger, Christian / Joiner, Joe D / Karlsson, Elin / Andersson, Eva / Chi, Celestine N / Andersson, Siv G E / Jemth, Per

    Journal of molecular biology

    2024  Volume 436, Issue 6, Page(s) 168490

    Abstract: The emergence of new proteins is a central question in biology. Most tertiary protein folds known to date appear to have an ancient origin, but it is clear from bioinformatic analyses that new proteins continuously emerge in all organismal groups. ... ...

    Abstract The emergence of new proteins is a central question in biology. Most tertiary protein folds known to date appear to have an ancient origin, but it is clear from bioinformatic analyses that new proteins continuously emerge in all organismal groups. However, there is a paucity of experimental data on new proteins regarding their structure and biophysical properties. We performed a detailed phylogenetic analysis and identified 48 putative open reading frames in the honeybee-associated bacterium Apilactobacillus kunkeei for which no or few homologs could be identified in closely-related species, suggesting that they could be relatively new on an evolutionary time scale and represent recently evolved proteins. Using circular dichroism-, fluorescence- and nuclear magnetic resonance (NMR) spectroscopy we investigated six of these proteins and show that they are not intrinsically disordered, but populate alpha-helical dominated folded states with relatively low thermodynamic stability (0-3 kcal/mol). The NMR and biophysical data demonstrate that small new proteins readily adopt simple folded conformations suggesting that more complex tertiary structures can be continuously re-invented during evolution by fusion of such simple secondary structure elements. These findings have implications for the general view on protein evolution, where de novo emergence of folded proteins may be a common event.
    MeSH term(s) Animals ; Circular Dichroism ; Lactobacillaceae ; Magnetic Resonance Spectroscopy ; Phylogeny ; Protein Conformation, alpha-Helical ; Protein Folding ; Thermodynamics ; Bacterial Proteins/chemistry
    Chemical Substances Bacterial Proteins
    Language English
    Publishing date 2024-02-13
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2024.168490
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 867: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  7. Article: The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns.

    Seeger, Christian / Dyrhage, Karl / Mahajan, Mayank / Odelgard, Anna / Lind, Sara Bergström / Andersson, Siv G E

    Frontiers in microbiology

    2021  Volume 12, Page(s) 643045

    Abstract: ... ...

    Abstract The
    Language English
    Publishing date 2021-05-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.643045
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  8. Article ; Online: Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum.

    Mahajan, Mayank / Seeger, Christian / Yee, Benjamin / Andersson, Siv G E

    Genome biology and evolution

    2020  Volume 12, Issue 9, Page(s) 1528–1548

    Abstract: Bacteria of the Planctomycetes phylum have many unique cellular features, such as extensive membrane invaginations and the ability to import macromolecules. These features raise intriguing questions about the composition of their cell envelopes. In this ... ...

    Abstract Bacteria of the Planctomycetes phylum have many unique cellular features, such as extensive membrane invaginations and the ability to import macromolecules. These features raise intriguing questions about the composition of their cell envelopes. In this study, we have used microscopy, phylogenomics, and proteomics to examine the composition and evolution of cell envelope proteins in Tuwongella immobilis and other members of the Planctomycetes. Cryo-electron tomography data indicated a distance of 45 nm between the inner and outer membranes in T. immobilis. Consistent with the wide periplasmic space, our bioinformatics studies showed that the periplasmic segments of outer-membrane proteins in type II secretion systems are extended in bacteria of the order Planctomycetales. Homologs of two highly abundant cysteine-rich cell wall proteins in T. immobilis were identified in all members of the Planctomycetales, whereas genes for peptidoglycan biosynthesis and cell elongation have been lost in many members of this bacterial group. The cell wall proteins contain multiple copies of the YTV motif, which is the only domain that is conserved and unique to the Planctomycetales. Earlier diverging taxa in the Planctomycetes phylum contain genes for peptidoglycan biosynthesis but no homologs to the YTV cell wall proteins. The major remodeling of the cell envelope in the ancestor of the Planctomycetales coincided with the emergence of budding and other unique cellular phenotypes. The results have implications for hypotheses about the process whereby complex cellular features evolve in bacteria.
    MeSH term(s) Bacterial Proteins/genetics ; Biological Evolution ; Peptidoglycan/biosynthesis ; Planctomycetales/genetics ; Planctomycetales/ultrastructure ; Protein Domains
    Chemical Substances Bacterial Proteins ; Peptidoglycan
    Language English
    Publishing date 2020-08-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1759-6653
    ISSN (online) 1759-6653
    DOI 10.1093/gbe/evaa159
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  9. Article ; Online: Letter to the editor concerning "Comment to chronic low back pain, bacterial infection and treatment with antibiotics".

    Fritzell, Peter / Bergström, Tomas / Andersson, Siv G E / Jönsson, Bodil / Skorpil, Mikael / Udby, Peter / Andersen, Mikkel / Hägg, Olle

    The spine journal : official journal of the North American Spine Society

    2021  Volume 21, Issue 7, Page(s) 1233–1235

    MeSH term(s) Anti-Bacterial Agents/adverse effects ; Bacterial Infections/drug therapy ; Humans ; Intervertebral Disc Displacement/drug therapy ; Low Back Pain/drug therapy
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2021-07-10
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 2037072-6
    ISSN 1878-1632 ; 1529-9430
    ISSN (online) 1878-1632
    ISSN 1529-9430
    DOI 10.1016/j.spinee.2021.03.035
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 5898: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article ; Online: Antibiotics should not be used for back/leg pain.

    Fritzell, Peter / Hägg, Olle / Bergström, Tomas / Jönsson, Bodil / Andersson, Siv G E / Skorpil, Mikael / Udby, Peter Muhareb / Andersen, Mikkel

    Acta orthopaedica

    2021  Volume 92, Issue 2, Page(s) 244–246

    MeSH term(s) Anti-Bacterial Agents/therapeutic use ; Back Pain/drug therapy ; Humans ; Leg
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2021-01-19
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 2180677-9
    ISSN 1745-3682 ; 1745-3674
    ISSN (online) 1745-3682
    ISSN 1745-3674
    DOI 10.1080/17453674.2020.1871190
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Uk I Zs.99: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top