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  1. Article ; Online: Decrypting the functional design of unmodified translation elongation factor P.

    Tomasiunaite, Urte / Kielkowski, Pavel / Krafczyk, Ralph / Forné, Ignasi / Imhof, Axel / Jung, Kirsten

    Cell reports

    2024  Volume 43, Issue 5, Page(s) 114063

    Abstract: Bacteria overcome ribosome stalling by employing translation elongation factor P (EF-P), which requires post-translational modification (PTM) for its full activity. However, EF-Ps of the PGKGP subfamily are unmodified. The mechanism behind the ability to ...

    Abstract Bacteria overcome ribosome stalling by employing translation elongation factor P (EF-P), which requires post-translational modification (PTM) for its full activity. However, EF-Ps of the PGKGP subfamily are unmodified. The mechanism behind the ability to avoid PTM while retaining active EF-P requires further examination. Here, we investigate the design principles governing the functionality of unmodified EF-Ps in Escherichia coli. We screen for naturally unmodified EF-Ps with activity in E. coli and discover that the EF-P from Rhodomicrobium vannielii rescues growth defects of a mutant lacking the modification enzyme EF-P-(R)-β-lysine ligase. We identify amino acids in unmodified EF-P that modulate its activity. Ultimately, we find that substitution of these amino acids in other marginally active EF-Ps of the PGKGP subfamily leads to fully functional variants in E. coli. These results provide strategies to improve heterologous expression of proteins with polyproline motifs in E. coli and give insights into cellular adaptations to optimize protein synthesis.
    Language English
    Publishing date 2024-04-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2024.114063
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online ; Thesis: Data analysis for genomics, transcriptomics and proteomics

    Sun, Bo [Verfasser] / Imhof, Axel [Akademischer Betreuer]

    2023  

    Author's details Bo Sun ; Betreuer: Axel Imhof
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Universitätsbibliothek der Ludwig-Maximilians-Universität
    Publishing place München
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  3. Article: Discovery of Native Protein Complexes by Liquid Chromatography Followed by Quantitative Mass Spectrometry.

    Aftab, Wasim / Imhof, Axel

    Advances in experimental medicine and biology

    2021  Volume 1336, Page(s) 105–128

    Abstract: Discovering protein complexes in vivo is of vital importance to understand the evolution and function of biological systems. Proteomics analysis has evolved as a state-of-the-art technique in elucidating the above information. A combination of liquid ... ...

    Abstract Discovering protein complexes in vivo is of vital importance to understand the evolution and function of biological systems. Proteomics analysis has evolved as a state-of-the-art technique in elucidating the above information. A combination of liquid chromatography (LC) and liquid chromatography coupled to shotgun mass spectrometry (LC-MS) provides the most exhaustive information in this regard. However, a significant amount of computational effort is required for the meaningful interpretation of the generated datasets. In this chapter we describe in detail the state-of-the-art pipeline to discover soluble protein complexes and provide practical advice focusing on typical situations a biologist faces while analyzing such proteomics datasets. Furthermore, we briefly describe two commonly used software packages to solve the described problem: Weka for training protein-protein interactions (PPIs) using machine learning (ML) and Cytoscape for clustering the interaction network.
    MeSH term(s) Chromatography, Liquid ; Mass Spectrometry ; Proteomics
    Language English
    Publishing date 2021-10-09
    Publishing country United States
    Document type Journal Article
    ISSN 2214-8019 ; 0065-2598
    ISSN (online) 2214-8019
    ISSN 0065-2598
    DOI 10.1007/978-3-030-77252-9_6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Thesis: Regulation des Transkriptionsfaktors AP-2 während zellulärer Differenzierung und Proliferation

    Imhof, Axel

    1995  

    Author's details vorgelegt von Axel Imhof
    Language German
    Size VI, 117 S. : Ill., graph. Darst.
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Regensburg, Univ., Diss., 1995
    HBZ-ID HT007131401
    Database Catalogue ZB MED Medicine, Health

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  5. Article ; Online: ImShot: An Open-Source Software for Probabilistic Identification of Proteins In Situ and Visualization of Proteomics Data.

    Aftab, Wasim / Lahiri, Shibojyoti / Imhof, Axel

    Molecular & cellular proteomics : MCP

    2022  Volume 21, Issue 6, Page(s) 100242

    Abstract: Imaging mass spectrometry (IMS) has developed into a powerful tool allowing label-free detection of numerous biomolecules in situ. In contrast to shotgun proteomics, proteins/peptides can be detected directly from biological tissues and correlated to its ...

    Abstract Imaging mass spectrometry (IMS) has developed into a powerful tool allowing label-free detection of numerous biomolecules in situ. In contrast to shotgun proteomics, proteins/peptides can be detected directly from biological tissues and correlated to its morphology leading to a gain of crucial clinical information. However, direct identification of the detected molecules is currently challenging for MALDI-IMS, thereby compelling researchers to use complementary techniques and resource intensive experimental setups. Despite these strategies, sufficient information could not be extracted because of lack of an optimum data combination strategy/software. Here, we introduce a new open-source software ImShot that aims at identifying peptides obtained in MALDI-IMS. This is achieved by combining information from IMS and shotgun proteomics (LC-MS) measurements of serial sections of the same tissue. The software takes advantage of a two-group comparison to determine the search space of IMS masses after deisotoping the corresponding spectra. Ambiguity in annotations of IMS peptides is eliminated by introduction of a novel scoring system that identifies the most likely parent protein of a detected peptide in the corresponding IMS dataset. Thanks to its modular structure, the software can also handle LC-MS data separately and display interactive enrichment plots and enriched Gene Ontology terms or cellular pathways. The software has been built as a desktop application with a conveniently designed graphic user interface to provide users with a seamless experience in data analysis. ImShot can run on all the three major desktop operating systems and is freely available under Massachusetts Institute of Technology license.
    MeSH term(s) Peptides/analysis ; Proteins/analysis ; Proteomics/methods ; Software ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
    Chemical Substances Peptides ; Proteins
    Language English
    Publishing date 2022-05-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2075924-1
    ISSN 1535-9484 ; 1535-9476
    ISSN (online) 1535-9484
    ISSN 1535-9476
    DOI 10.1016/j.mcpro.2022.100242
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online ; Thesis: Computational methods for exploratory analysis of proteomics data

    Aftab, Wasim [Verfasser] / Imhof, Axel [Akademischer Betreuer]

    2022  

    Author's details Wasim Aftab ; Betreuer: Axel Imhof
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Universitätsbibliothek der Ludwig-Maximilians-Universität
    Publishing place München
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  7. Book ; Online ; Thesis: The measurement of S-adenosyl methionine in situ

    Hartmann, Lennart Verfasser] / [Imhof, Axel [Akademischer Betreuer]

    2022  

    Author's details Lennart Hartmann ; Betreuer: Axel Imhof
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Universitätsbibliothek der Ludwig-Maximilians-Universität
    Publishing place München
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  8. Article ; Online: Ribosome inactivation regulates translation elongation in neurons.

    Popper, Bastian / Bürkle, Martina / Ciccopiedi, Giuliana / Marchioretto, Marta / Forné, Ignasi / Imhof, Axel / Straub, Tobias / Viero, Gabriella / Götz, Magdalena / Schieweck, Rico

    The Journal of biological chemistry

    2024  Volume 300, Issue 2, Page(s) 105648

    Abstract: Cellular plasticity is crucial for adapting to ever-changing stimuli. As a result, cells consistently reshape their translatome, and, consequently, their proteome. The control of translational activity has been thoroughly examined at the stage of ... ...

    Abstract Cellular plasticity is crucial for adapting to ever-changing stimuli. As a result, cells consistently reshape their translatome, and, consequently, their proteome. The control of translational activity has been thoroughly examined at the stage of translation initiation. However, the regulation of ribosome speed in cells is widely unknown. In this study, we utilized a timed ribosome runoff approach, along with proteomics and transmission electron microscopy, to investigate global translation kinetics in cells. We found that ribosome speeds vary among various cell types, such as astrocytes, induced pluripotent human stem cells, human neural stem cells, and human and rat neurons. Of all cell types studied, mature cortical neurons exhibit the highest rate of translation. This finding is particularly remarkable because mature cortical neurons express the eukaryotic elongation factor 2 (eEF2) at lower levels than other cell types. Neurons solve this conundrum by inactivating a fraction of their ribosomes. As a result, the increase in eEF2 levels leads to a reduction of inactive ribosomes and an enhancement of active ones. Processes that alter the demand for active ribosomes, like neuronal excitation, cause increased inactivation of redundant ribosomes in an eEF2-dependent manner. Our data suggest a novel regulatory mechanism in which neurons dynamically inactivate ribosomes to facilitate translational remodeling. These findings have important implications for developmental brain disorders characterized by, among other things, aberrant translation.
    MeSH term(s) Animals ; Humans ; Rats ; Neurons/metabolism ; Protein Biosynthesis ; Protein Processing, Post-Translational ; Ribosomes/metabolism ; Mice ; Mice, Inbred C57BL
    Language English
    Publishing date 2024-01-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2024.105648
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Processivity and specificity of histone acetylation by the male-specific lethal complex.

    Kiss, Anna E / Venkatasubramani, Anuroop V / Pathirana, Dilan / Krause, Silke / Sparr, Aline Campos / Hasenauer, Jan / Imhof, Axel / Müller, Marisa / Becker, Peter B

    Nucleic acids research

    2024  

    Abstract: Acetylation of lysine 16 of histone H4 (H4K16ac) stands out among the histone modifications, because it decompacts the chromatin fiber. The metazoan acetyltransferase MOF (KAT8) regulates transcription through H4K16 acetylation. Antibody-based studies ... ...

    Abstract Acetylation of lysine 16 of histone H4 (H4K16ac) stands out among the histone modifications, because it decompacts the chromatin fiber. The metazoan acetyltransferase MOF (KAT8) regulates transcription through H4K16 acetylation. Antibody-based studies had yielded inconclusive results about the selectivity of MOF to acetylate the H4 N-terminus. We used targeted mass spectrometry to examine the activity of MOF in the male-specific lethal core (4-MSL) complex on nucleosome array substrates. This complex is part of the Dosage Compensation Complex (DCC) that activates X-chromosomal genes in male Drosophila. During short reaction times, MOF acetylated H4K16 efficiently and with excellent selectivity. Upon longer incubation, the enzyme progressively acetylated lysines 12, 8 and 5, leading to a mixture of oligo-acetylated H4. Mathematical modeling suggests that MOF recognizes and acetylates H4K16 with high selectivity, but remains substrate-bound and continues to acetylate more N-terminal H4 lysines in a processive manner. The 4-MSL complex lacks non-coding roX RNA, a critical component of the DCC. Remarkably, addition of RNA to the reaction non-specifically suppressed H4 oligo-acetylation in favor of specific H4K16 acetylation. Because RNA destabilizes the MSL-nucleosome interaction in vitro we speculate that RNA accelerates enzyme-substrate turn-over in vivo, thus limiting the processivity of MOF, thereby increasing specific H4K16 acetylation.
    Language English
    Publishing date 2024-02-26
    Publishing country England
    Document type Journal Article
    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/gkae123
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online ; Thesis: Die Bestimmung der Histon H4-Acetylierungsmuster in PBMCs im Alterungsprozess des Menschen mittels Massenspektrometrie

    Bux, Esther Marie [Verfasser] / Imhof, Axel [Akademischer Betreuer]

    2022  

    Author's details Esther Marie Bux ; Betreuer: Axel Imhof
    Keywords Medizin, Gesundheit ; Medicine, Health
    Subject code sg610
    Language German
    Publisher Universitätsbibliothek der Ludwig-Maximilians-Universität
    Publishing place München
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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