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  1. AU="Stülke, Jörg"
  2. AU="Tran Kiem, Cécile"
  3. AU="Trivedi, Pritesh S"
  4. AU="Seemann, Stefan E"
  5. AU="Lotfi Chouchane"
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  9. AU="Bruno Alessandro Rivieccio"
  10. AU="Cristea, Alexandra I"
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  13. AU="Raza Naqvi"
  14. AU="Chin Fatt, Cherise R"
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  1. Book ; Online: Regulatory potential of post-translational modifications in bacteria

    Mijakovic, Ivan / Grangeasse, Christophe / Stulke, Jorg

    2015  

    Abstract: Post-translational modifications (PTMs) are widely employed by all living organisms to control the enzymatic activity, localization or stability of proteins on a much shorter time scale than the transcriptional control. In eukarya, global analyses ... ...

    Abstract Post-translational modifications (PTMs) are widely employed by all living organisms to control the enzymatic activity, localization or stability of proteins on a much shorter time scale than the transcriptional control. In eukarya, global analyses consistently reveal that proteins are very extensively phosphorylated, acetylated and ubiquitylated. Glycosylation and methylation are also very common, and myriad other PTMs, most with a proven regulatory potential, are being discovered continuously. The emergent picture is that PTM sites on a single protein are not independent; modification of one residue often affects (positively or negatively) modification of other sites on the same protein.-

    The best example of this complex behavior is the histone "bar-code" with very extensive cross-talk between phosphorylation, acetylation and methylation sites.Traditionally it was believed that large networks of PTMs exist only in complex eukaryal cells, which exploit them for coordination and fine-tuning of various cellular functions. PTMs have also been detected in bacteria, but the early examples focused on a few important regulatory events, based mainly on protein phosphorylation. The global importance (and abundance) of PTMs in bacterial physiology was systematically underestimated. In recent years, global studies have reported large datasets of phosphorylated, acetylated and glycosylated proteins in bacteria. Other modifications of bacterial proteins have been recently described: pupylation, methylation, sirtuin acetylation, lipidation, carboxylation and bacillithiolation.-

    As the landscape of PTMs in bacterial cells is rapidly expanding, primarily due to advances of detection methods in mass spectrometry, our research field is adapting to comprehend the potential impact of these modifications on the cellular physiology. The field of protein phosphorylation, especially of the Ser/Thr/Tyr type, has been profoundly transformed. We have become aware that bacterial kinases phosphorylate many protein substrates and thus constitute regulatory nodes with potential for signal integration. They also engage in cross-talk and eukaryal-like mutual activation cascades. The regulatory potential of protein acetylation and glycosylation in bacteria is also rapidly emerging, and the cross-talk between acetylation and phosphorylation has been documented. This topic deals with the complexity of the PTM landscape in bacteria, and focus in particular on the physiological roles that PTMs play and methods to study them.-
    Keywords Science (General) ; Microbiology
    Size 1 electronic resource (204 p.)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT020091805
    ISBN 9782889196104 ; 2889196100
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: PAE viewer: a webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks.

    Elfmann, Christoph / Stülke, Jörg

    Nucleic acids research

    2023  Volume 51, Issue W1, Page(s) W404–W410

    Abstract: The development of AlphaFold for protein structure prediction has opened a new era in structural biology. This is even more the case for AlphaFold-Multimer for the prediction of protein complexes. The interpretation of these predictions has become more ... ...

    Abstract The development of AlphaFold for protein structure prediction has opened a new era in structural biology. This is even more the case for AlphaFold-Multimer for the prediction of protein complexes. The interpretation of these predictions has become more important than ever, but it is difficult for the non-specialist. While an evaluation of the prediction quality is provided for monomeric protein predictions by the AlphaFold Protein Structure Database, such a tool is missing for predicted complex structures. Here, we present the PAE Viewer webserver (http://www.subtiwiki.uni-goettingen.de/v4/paeViewerDemo), an online tool for the integrated visualization of predicted protein complexes using a 3D structure display combined with an interactive representation of the Predicted Aligned Error (PAE). This metric allows an estimation of the quality of the prediction. Importantly, our webserver also allows the integration of experimental cross-linking data which helps to interpret the reliability of the structure predictions. With the PAE Viewer, the user obtains a unique online tool which for the first time allows the intuitive evaluation of the PAE for protein complex structure predictions with integrated crosslinks.
    MeSH term(s) Computational Chemistry/methods ; Databases, Protein ; Internet ; Models, Molecular ; Protein Structure, Tertiary ; Proteins/chemistry ; Reproducibility of Results ; Software ; User-Computer Interface
    Chemical Substances Proteins
    Language English
    Publishing date 2023-05-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad350
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Control of three-carbon amino acid homeostasis by promiscuous importers and exporters in

    Warneke, Robert / Herzberg, Christina / Daniel, Richard / Hormes, Björn / Stülke, Jörg

    mBio

    2024  Volume 15, Issue 4, Page(s) e0345623

    Abstract: The Gram-positive model ... ...

    Abstract The Gram-positive model bacterium
    MeSH term(s) Amino Acids/metabolism ; Bacillus subtilis/metabolism ; Bacterial Proteins/metabolism ; Homeostasis ; Amino Acid Transport Systems ; beta-Alanine/metabolism
    Chemical Substances Amino Acids ; Bacterial Proteins ; Amino Acid Transport Systems ; beta-Alanine (11P2JDE17B)
    Language English
    Publishing date 2024-03-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.03456-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online ; Thesis: Amino acid metabolism in Bacillus subtilis

    Meißner, Janek [Verfasser] / Stülke, Jörg [Akademischer Betreuer] / Stülke, Jörg [Gutachter] / Daniel, Rolf [Gutachter]

    2024  

    Author's details Janek Meißner ; Gutachter: Jörg Stülke, Rolf Daniel ; Betreuer: Jörg Stülke
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Niedersächsische Staats- und Universitätsbibliothek Göttingen
    Publishing place Göttingen
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  5. Article ; Online: The many roles of cyclic di-AMP to control the physiology of

    Herzberg, Christina / Meißner, Janek / Warneke, Robert / Stülke, Jörg

    microLife

    2023  Volume 4, Page(s) uqad043

    Abstract: The dinucleotide cyclic di-AMP (c-di-AMP) is synthesized as a second messenger in the Gram-positive model ... ...

    Abstract The dinucleotide cyclic di-AMP (c-di-AMP) is synthesized as a second messenger in the Gram-positive model bacterium
    Language English
    Publishing date 2023-10-20
    Publishing country England
    Document type Journal Article ; Review
    ISSN 2633-6693
    ISSN (online) 2633-6693
    DOI 10.1093/femsml/uqad043
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Bacillus subtilis, a Swiss Army Knife in Science and Biotechnology.

    Stülke, Jörg / Grüppen, Anika / Bramkamp, Marc / Pelzer, Stefan

    Journal of bacteriology

    2023  Volume 205, Issue 5, Page(s) e0010223

    Abstract: Next to Escherichia coli, Bacillus subtilis is the most studied and best understood organism that also serves as a model for many important pathogens. Due to its ability to form heat-resistant spores that can germinate even after very long periods of ... ...

    Abstract Next to Escherichia coli, Bacillus subtilis is the most studied and best understood organism that also serves as a model for many important pathogens. Due to its ability to form heat-resistant spores that can germinate even after very long periods of time, B. subtilis has attracted much scientific interest. Another feature of B. subtilis is its genetic competence, a developmental state in which B. subtilis actively takes up exogenous DNA. This makes B. subtilis amenable to genetic manipulation and investigation. The bacterium was one of the first with a fully sequenced genome, and it has been subject to a wide variety of genome- and proteome-wide studies that give important insights into many aspects of the biology of B. subtilis. Due to its ability to secrete large amounts of proteins and to produce a wide range of commercially interesting compounds, B. subtilis has become a major workhorse in biotechnology. Here, we review the development of important aspects of the research on B. subtilis with a specific focus on its cell biology and biotechnological and practical applications from vitamin production to concrete healing. The intriguing complexity of the developmental programs of B. subtilis, paired with the availability of sophisticated tools for genetic manipulation, positions it at the leading edge for discovering new biological concepts and deepening our understanding of the organization of bacterial cells.
    MeSH term(s) Bacillus subtilis/metabolism ; Biotechnology ; Spores, Bacterial/genetics
    Language English
    Publishing date 2023-05-04
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/jb.00102-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: ListiWiki: A database for the foodborne pathogen Listeria monocytogenes.

    Elfmann, Christoph / Zhu, Bingyao / Stülke, Jörg / Halbedel, Sven

    International journal of medical microbiology : IJMM

    2023  Volume 313, Issue 6, Page(s) 151591

    Abstract: Listeria monocytogenes is a Gram positive foodborne pathogen that regularly causes outbreaks of systemic infectious diseases. The bacterium maintains a facultative intracellular lifestyle; it thrives under a variety of environmental conditions and is ... ...

    Abstract Listeria monocytogenes is a Gram positive foodborne pathogen that regularly causes outbreaks of systemic infectious diseases. The bacterium maintains a facultative intracellular lifestyle; it thrives under a variety of environmental conditions and is able to infect human host cells. L. monocytogenes is genetically tractable and therefore has become an attractive model system to study the mechanisms employed by facultative intracellular bacteria to invade eukaryotic cells and to replicate in their cytoplasm. Besides its importance for basic research, L. monocytogenes also serves as a paradigmatic pathogen in genomic epidemiology, where the relative stability of its genome facilitates successful outbreak detection and elucidation of transmission chains in genomic pathogen surveillance systems. In both terms, it is necessary to keep the annotation of the L. monocytogenes genome up to date. Therefore, we have created the database ListiWiki (http://listiwiki.uni-goettingen.de/) which stores comprehensive information on the widely used L. monocytogenes reference strain EDG-e. ListiWiki is designed to collect information on genes, proteins and RNAs and their relevant functional characteristics, but also further information such as mutant phenotypes, available biological material, and publications. In its present form, ListiWiki combines the most recent annotation of the EDG-e genome with published data on gene essentiality, gene expression and subcellular protein localization. ListiWiki also predicts protein-protein interactions networks based on protein homology to Bacillus subtilis proteins, for which detailed interaction maps have been compiled in the sibling database SubtiWiki. Furthermore, crystallographic information of proteins is made accessible through integration of Protein Structure Database codes and AlphaFold structure predictions. ListiWiki is an easy-to-use web interface that has been developed with a focus on an intuitive access to all information. Use of ListiWiki is free of charge and its content can be edited by all members of the scientific community after registration. In our labs, ListiWiki has already become an important and easy to use tool to quickly access genome annotation details that we can keep updated with advancing knowledge. It also might be useful to promote the comprehensive understanding of the physiology and virulence of an important human pathogen.
    MeSH term(s) Humans ; Listeria monocytogenes/genetics ; Genes, Bacterial ; Protein Interaction Maps ; Genomics ; Listeriosis/epidemiology ; Bacterial Proteins/genetics
    Chemical Substances Bacterial Proteins
    Language English
    Publishing date 2023-11-29
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2006518-8
    ISSN 1618-0607 ; 1438-4221
    ISSN (online) 1618-0607
    ISSN 1438-4221
    DOI 10.1016/j.ijmm.2023.151591
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Recent advances and perspectives in nucleotide second messenger signaling in bacteria.

    Hengge, Regine / Pruteanu, Mihaela / Stülke, Jörg / Tschowri, Natalia / Turgay, Kürşad

    microLife

    2023  Volume 4, Page(s) uqad015

    Abstract: Nucleotide second messengers act as intracellular 'secondary' signals that represent environmental or cellular cues, i.e. the 'primary' signals. As such, they are linking sensory input with regulatory output in all living cells. The amazing physiological ...

    Abstract Nucleotide second messengers act as intracellular 'secondary' signals that represent environmental or cellular cues, i.e. the 'primary' signals. As such, they are linking sensory input with regulatory output in all living cells. The amazing physiological versatility, the mechanistic diversity of second messenger synthesis, degradation, and action as well as the high level of integration of second messenger pathways and networks in prokaryotes has only recently become apparent. In these networks, specific second messengers play conserved general roles. Thus, (p)ppGpp coordinates growth and survival in response to nutrient availability and various stresses, while c-di-GMP is
    Language English
    Publishing date 2023-04-17
    Publishing country England
    Document type Journal Article ; Review
    ISSN 2633-6693
    ISSN (online) 2633-6693
    DOI 10.1093/femsml/uqad015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Understudied proteins and understudied functions in the model bacterium Bacillus subtilis-A major challenge in current research.

    Wicke, Dennis / Meißner, Janek / Warneke, Robert / Elfmann, Christoph / Stülke, Jörg

    Molecular microbiology

    2023  Volume 120, Issue 1, Page(s) 8–19

    Abstract: Model organisms such as the Gram-positive bacterium Bacillus subtilis have been studied intensively for decades. However, even for model organisms, no function has been identified for about one fourth of all proteins. It has recently been realized that ... ...

    Abstract Model organisms such as the Gram-positive bacterium Bacillus subtilis have been studied intensively for decades. However, even for model organisms, no function has been identified for about one fourth of all proteins. It has recently been realized that such understudied proteins as well as poorly studied functions set a limitation to our understanding of the requirements for cellular life, and the Understudied Proteins Initiative has been launched. Of poorly studied proteins, those that are strongly expressed are likely to be important to the cell and should therefore be considered high priority in further studies. Since the functional analysis of unknown proteins can be extremely laborious, a minimal knowledge is required prior to targeted functional studies. In this review, we discuss strategies to obtain such a minimal annotation, for example, from global interaction, expression, or localization studies. We present a set of 41 highly expressed and poorly studied proteins of B. subtilis. Several of these proteins are thought or known to bind RNA and/or the ribosome, some may control the metabolism of B. subtilis, and another subset of particularly small proteins may act as regulatory elements to control the expression of downstream genes. Moreover, we discuss the challenges of poorly studied functions with a focus on RNA-binding proteins, amino acid transport, and the control of metabolic homeostasis. The identification of the functions of the selected proteins not only will strongly advance our knowledge on B. subtilis, but also on other organisms since many of the proteins are conserved in many groups of bacteria.
    MeSH term(s) Bacillus subtilis/genetics ; Bacillus subtilis/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biological Transport ; Ribosomes/metabolism ; Homeostasis
    Chemical Substances Bacterial Proteins
    Language English
    Publishing date 2023-03-15
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 619315-8
    ISSN 1365-2958 ; 0950-382X
    ISSN (online) 1365-2958
    ISSN 0950-382X
    DOI 10.1111/mmi.15053
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online ; Thesis: Validation of novel protein-protein interactions in Bacillus subtilis

    Bremenkamp, Rica [Verfasser] / Stülke, Jörg [Akademischer Betreuer] / Stülke, Jörg [Gutachter] / Ficner, Ralf [Gutachter] / Feußner, Ivo [Gutachter]

    2023  

    Author's details Rica Bremenkamp ; Gutachter: Jörg Stülke, Ralf Ficner, Ivo Feußner ; Betreuer: Jörg Stülke
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Niedersächsische Staats- und Universitätsbibliothek Göttingen
    Publishing place Göttingen
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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