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  1. Book: Proteostasis and disease

    Barrio, Rosa / Sutherland, James D. / Rodríguez, Manuel S.

    from basic mechanisms to clinics

    (Advances in experimental medicine and biology ; 1233)

    2020  

    Author's details Rosa Barrio, James Sutherland, Manuel Rodriguez editors
    Series title Advances in experimental medicine and biology ; 1233
    Collection
    Language English
    Size xii, 348 Seiten, Illustrationen
    Publisher Springer
    Publishing place Cham
    Publishing country Switzerland
    Document type Book
    HBZ-ID HT020436960
    ISBN 978-3-030-38265-0 ; 9783030382667 ; 3-030-38265-6 ; 3030382664
    Database Catalogue ZB MED Medicine, Health

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  2. Article ; Online: SUMO-ID: A Strategy for the Identification of SUMO-Dependent Proximal Interactors.

    Barroso-Gomila, Orhi / Mayor, Ugo / Barrio, Rosa / Sutherland, James D

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2602, Page(s) 177–189

    Abstract: Posttranslational modifications by the ubiquitin-like family (UbL) of proteins determine the biological fate of a substrate, including new interaction partners. In the case of the small ubiquitin-like modifier (SUMO), this is achieved in part through its ...

    Abstract Posttranslational modifications by the ubiquitin-like family (UbL) of proteins determine the biological fate of a substrate, including new interaction partners. In the case of the small ubiquitin-like modifier (SUMO), this is achieved in part through its non-covalent interaction with SUMO-interacting motifs (SIMs) found in some proteins. Investigating such partner-complex formation is particularly challenging due to the fast dynamics and reversibility of SUMO modifications and the low affinity of SUMO-SIM interactions. Here, we present a detailed protocol of SUMO-ID, a technology that merges promiscuous proximity biotinylation by TurboID enzyme and protein-fragment complementation strategy to specifically biotinylate SUMO-dependent interactors of particular substrates. When coupled to streptavidin-affinity purification and mass spectrometry, SUMO-ID efficiently identifies SUMO-dependent interactors of a given protein. The methodology describes all the steps from SUMO-ID cell line generation to LC-MS sample preparation to study SUMO-dependent interactors of a particular protein. The protocol is generic and therefore adaptable to study other UbL-dependent interactors, such as ubiquitin.
    MeSH term(s) Ubiquitin ; Protein Processing, Post-Translational ; Mass Spectrometry ; Biotinylation ; Cell Line
    Chemical Substances Ubiquitin
    Language English
    Publishing date 2022-11-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2859-1_13
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Biotin-Based Strategies to Explore the World of Ubiquitin and Ubiquitin-Like Modifiers.

    Merino-Cacho, Laura / Barroso-Gomila, Orhi / Hernández-Sánchez, Sandra / Ramirez, Juanma / Mayor, Ugo / Sutherland, James D / Barrio, Rosa

    Chembiochem : a European journal of chemical biology

    2024  Volume 25, Issue 6, Page(s) e202300746

    Abstract: A complex code of cellular signals is mediated by ubiquitin and ubiquitin-like (Ub/UbL) modifications on substrate proteins. The so-called Ubiquitin Code specifies protein fates, such as stability, subcellular localization, functional activation or ... ...

    Abstract A complex code of cellular signals is mediated by ubiquitin and ubiquitin-like (Ub/UbL) modifications on substrate proteins. The so-called Ubiquitin Code specifies protein fates, such as stability, subcellular localization, functional activation or suppression, and interactions. Hundreds of enzymes are involved in placing and removing Ub/UbL on thousands of substrates, while the consequences of modifications and the mechanisms of specificity are still poorly defined. Challenges include rapid and transient engagement of enzymes and Ub/UbL interactors, low stoichiometry of modified versus non-modified cellular substrates, and protease-mediated loss of Ub/UbL in lysates. To decipher this complexity and confront the challenges, many tools have been created to trap and identify substrates and interactors linked to Ub/UbL modification. This review focuses on an assortment of biotin-based tools developed for this purpose (for example BioUbLs, UbL-ID, BioE3, BioID), taking advantage of the strong affinity of biotin-streptavidin and the stringent lysis/washing approach allowed by it, paired with sensitive mass-spectrometry-based proteomic methods. Knowing how substrates change during development and disease, the consequences of substrate modification, and matching substrates to particular UbL-ligating enzymes will contribute new insights into how Ub/UbL signaling works and how it can be exploited for therapies.
    MeSH term(s) Ubiquitin/metabolism ; Biotin ; Proteomics ; Peptide Hydrolases
    Chemical Substances Ubiquitin ; Biotin (6SO6U10H04) ; Peptide Hydrolases (EC 3.4.-)
    Language English
    Publishing date 2024-01-05
    Publishing country Germany
    Document type Review ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020469-3
    ISSN 1439-7633 ; 1439-4227
    ISSN (online) 1439-7633
    ISSN 1439-4227
    DOI 10.1002/cbic.202300746
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  4. Article ; Online: Proteostasis: The network behind the networks.

    Barrio, Rosa / Sutherland, James D

    Seminars in cell & developmental biology

    2019  Volume 93, Page(s) 97–99

    MeSH term(s) Humans ; Metabolic Networks and Pathways ; Proteostasis ; Ubiquitin/metabolism
    Chemical Substances Ubiquitin
    Language English
    Publishing date 2019-04-21
    Publishing country England
    Document type Editorial ; Introductory Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1312473-0
    ISSN 1096-3634 ; 1084-9521
    ISSN (online) 1096-3634
    ISSN 1084-9521
    DOI 10.1016/j.semcdb.2019.04.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Proteostasis: the network behind the networks.

    Barrio, Rosa / Sutherland, James D

    Seminars in cell & developmental biology

    2019  

    Language English
    Publishing date 2019-05-09
    Publishing country England
    Document type Editorial
    ZDB-ID 1312473-0
    ISSN 1096-3634 ; 1084-9521
    ISSN (online) 1096-3634
    ISSN 1084-9521
    DOI 10.1016/j.semcdb.2019.05.005
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  6. Article ; Online: Putting the Stress on UFM1 (Ubiquitin-Fold Modifier 1).

    Sutherland, James D / Barrio, Rosa

    Circulation. Heart failure

    2018  Volume 11, Issue 10, Page(s) e005455

    MeSH term(s) Endoplasmic Reticulum Stress ; Heart Failure ; Homeostasis ; Humans ; Ligases ; Proteins ; Ubiquitins
    Chemical Substances Proteins ; UFM1 protein, human ; Ubiquitins ; Ligases (EC 6.-)
    Language English
    Publishing date 2018-10-30
    Publishing country United States
    Document type Editorial ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 2429459-7
    ISSN 1941-3297 ; 1941-3289
    ISSN (online) 1941-3297
    ISSN 1941-3289
    DOI 10.1161/CIRCHEARTFAILURE.118.005455
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Studying the ubiquitin code through biotin-based labelling methods

    Barroso-Gomila, Orhi / Muratore, Veronica / Merino-Cacho, Laura / Rodríguez, José Antonio / Barrio, Rosa / Sutherland, James D.

    Seminars in cell & developmental biology. 2022 Feb. 05,

    2022  

    Abstract: Post-translational modifications of cellular substrates by members of the ubiquitin (Ub) and ubiquitin-like (UbL) family are crucial for regulating protein homeostasis in organisms. The term "ubiquitin code" encapsulates how this diverse family of ... ...

    Abstract Post-translational modifications of cellular substrates by members of the ubiquitin (Ub) and ubiquitin-like (UbL) family are crucial for regulating protein homeostasis in organisms. The term "ubiquitin code" encapsulates how this diverse family of modifications, via adding single UbLs or different types of UbL chains, leads to specific fates for substrates. Cancer, neurodegeneration and other conditions are sometimes linked to underlying errors in this code. Studying these modifications in cells is particularly challenging since they are usually transient, scarce, and compartment-specific. Advances in the use of biotin-based methods to label modified proteins, as well as their proximally-located interactors, facilitate isolation and identification of substrates, modification sites, and the enzymes responsible for writing and erasing these modifications, as well as factors recruited as a consequence of the substrate being modified. In this review, we discuss site-specific and proximity biotinylation approaches being currently applied for studying modifications by UbLs, highlighting the pros and cons, with mention of complementary methods when possible. Future improvements may come from bioengineering and chemical biology but even now, biotin-based technology is uncovering new substrates and regulators, expanding potential therapeutic targets to manipulate the Ub code.
    Keywords Ubiquitin ; SUMO ; Proximity proteomics ; Biotin ; BirA
    Language English
    Dates of publication 2022-0205
    Publishing place Elsevier Ltd
    Document type Article ; Online
    Note Pre-press version
    ZDB-ID 1312473-0
    ISSN 1096-3634 ; 1084-9521
    ISSN (online) 1096-3634
    ISSN 1084-9521
    DOI 10.1016/j.semcdb.2022.02.009
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Studying the ubiquitin code through biotin-based labelling methods.

    Barroso-Gomila, Orhi / Muratore, Veronica / Merino-Cacho, Laura / Rodriguez, Jose Antonio / Barrio, Rosa / Sutherland, James D

    Seminars in cell & developmental biology

    2022  Volume 132, Page(s) 109–119

    Abstract: Post-translational modifications of cellular substrates by members of the ubiquitin (Ub) and ubiquitin-like (UbL) family are crucial for regulating protein homeostasis in organisms. The term "ubiquitin code" encapsulates how this diverse family of ... ...

    Abstract Post-translational modifications of cellular substrates by members of the ubiquitin (Ub) and ubiquitin-like (UbL) family are crucial for regulating protein homeostasis in organisms. The term "ubiquitin code" encapsulates how this diverse family of modifications, via adding single UbLs or different types of UbL chains, leads to specific fates for substrates. Cancer, neurodegeneration and other conditions are sometimes linked to underlying errors in this code. Studying these modifications in cells is particularly challenging since they are usually transient, scarce, and compartment-specific. Advances in the use of biotin-based methods to label modified proteins, as well as their proximally-located interactors, facilitate isolation and identification of substrates, modification sites, and the enzymes responsible for writing and erasing these modifications, as well as factors recruited as a consequence of the substrate being modified. In this review, we discuss site-specific and proximity biotinylation approaches being currently applied for studying modifications by UbLs, highlighting the pros and cons, with mention of complementary methods when possible. Future improvements may come from bioengineering and chemical biology but even now, biotin-based technology is uncovering new substrates and regulators, expanding potential therapeutic targets to manipulate the Ub code.
    MeSH term(s) Ubiquitin/metabolism ; Biotin/metabolism ; Protein Processing, Post-Translational ; Proteins/metabolism
    Chemical Substances Ubiquitin ; Biotin (6SO6U10H04) ; Proteins
    Language English
    Publishing date 2022-02-16
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1312473-0
    ISSN 1096-3634 ; 1084-9521
    ISSN (online) 1096-3634
    ISSN 1084-9521
    DOI 10.1016/j.semcdb.2022.02.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Preservation of the heart in ancient Egyptian mummies: A computed tomography investigation with focus on the myocardium.

    Panzer, Stephanie / Paladin, Alice / Zesch, Stephanie / Rosendahl, Wilfried / Augat, Peter / Thompson, Randall C / Miyamoto, Michael I / Sutherland, M Linda / Allam, Adel H / Wann, L Samuel / Sutherland, James D / Rowan, Chris J / Michalik, David E / Hergan, Klaus / Zink, Albert R

    Clinical anatomy (New York, N.Y.)

    2024  

    Abstract: The ancient Egyptians considered the heart to be the most important organ. The belief that the heart remained in the body is widespread in the archeological and paleopathological literature. The purpose of this study was to perform an overview of the ... ...

    Abstract The ancient Egyptians considered the heart to be the most important organ. The belief that the heart remained in the body is widespread in the archeological and paleopathological literature. The purpose of this study was to perform an overview of the preserved intrathoracic structures and thoracic and abdominal cavity filling, and to determine the prevalence and computed tomography (CT) characteristics of the myocardium in the preserved hearts of ancient Egyptian mummies. Whole-body CT examinations of 45 ancient Egyptian mummies (23 mummies from the Ägyptisches Museum und Papyrussammlung, Berlin, Germany, and 22 mummies from the Museo Egizio, Turin, Italy) were systematically assessed for preserved intrathoracic soft tissues including various anatomical components of the heart (pericardium, interventricular septum, four chambers, myocardium, valves). Additionally, evidence of evisceration and cavity filling was documented. In cases with identifiable myocardium, quantitative (measurements of thickness and density) and qualitative (description of the structure) assessment of the myocardial tissue was carried out. Heart structure was identified in 28 mummies (62%). In 33 mummies, CT findings demonstrated evisceration, with subsequent cavity filling in all but one case. Preserved myocardium was identified in nine mummies (five male, four female) as a mostly homogeneous, shrunken structure. The posterior wall of the myocardium had a mean maximum thickness of 3.6 mm (range 1.4-6.6 mm) and a mean minimum thickness of 1.0 mm (range 0.5-1.7 mm). The mean Hounsfield units (HU) of the myocardium at the posterior wall was 61 (range, 185-305). There was a strong correlation between the HU of the posterior wall of the myocardium and the mean HU of the muscles at the dorsal humerus (R = 0.77; p = 0.02). In two cases, there were postmortem changes in the myocardium, most probably due to insect infestation. To our knowledge, this is the first study to investigate the myocardium systematically on CT scans of ancient Egyptian mummies. Strong correlations between the densities of the myocardium and skeletal muscle indicated similar postmortem changes of the respective musculature during the mummification process within individual mummies. The distinct postmortem shrinking of the myocardium and the collapse of the left ventriclular cavity in several cases did not allow for paleopathological diagnoses such as myocardial scarring.
    Language English
    Publishing date 2024-04-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1025505-9
    ISSN 1098-2353 ; 0897-3806
    ISSN (online) 1098-2353
    ISSN 0897-3806
    DOI 10.1002/ca.24151
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  10. Article ; Online: SUMOylation modulates eIF5A activities in both yeast and pancreatic ductal adenocarcinoma cells.

    Seoane, Rocío / Lama-Díaz, Tomás / Romero, Antonia María / El Motiam, Ahmed / Martínez-Férriz, Arantxa / Vidal, Santiago / Bouzaher, Yanis H / Blanquer, María / Tolosa, Rocío M / Castillo Mewa, Juan / Rodríguez, Manuel S / García-Sastre, Adolfo / Xirodimas, Dimitris / Sutherland, James D / Barrio, Rosa / Alepuz, Paula / Blanco, Miguel G / Farràs, Rosa / Rivas, Carmen

    Cellular & molecular biology letters

    2024  Volume 29, Issue 1, Page(s) 15

    Abstract: Background: The eukaryotic translation initiation protein eIF5A is a highly conserved and essential factor that plays a critical role in different physiological and pathological processes including stress response and cancer. Different proteomic studies ...

    Abstract Background: The eukaryotic translation initiation protein eIF5A is a highly conserved and essential factor that plays a critical role in different physiological and pathological processes including stress response and cancer. Different proteomic studies suggest that eIF5A may be a small ubiquitin-like modifier (SUMO) substrate, but whether eIF5A is indeed SUMOylated and how relevant is this modification for eIF5A activities are still unknown.
    Methods: SUMOylation was evaluated using in vitro SUMOylation assays, Histidine-tagged proteins purification from His6-SUMO2 transfected cells, and isolation of endogenously SUMOylated proteins using SUMO-binding entities (SUBES). Mutants were engineered by site-directed mutagenesis. Protein stability was measured by a cycloheximide chase assay. Protein localization was determined using immunofluorescence and cellular fractionation assays. The ability of eIF5A1 constructs to complement the growth of Saccharomyces cerevisiae strains harboring thermosensitive mutants of a yeast EIF5A homolog gene (HYP2) was analyzed. The polysome profile and the formation of stress granules in cells expressing Pab1-GFP (a stress granule marker) by immunofluorescence were determined in yeast cells subjected to heat shock. Cell growth and migration of pancreatic ductal adenocarcinoma PANC-1 cells overexpressing different eIF5A1 constructs were evaluated using crystal violet staining and transwell inserts, respectively. Statistical analysis was performed with GraphPad Software, using unpaired Student's t-test, or one-way or two-way analysis of variance (ANOVA).
    Results: We found that eIF5A is modified by SUMO2 in vitro, in transfected cells and under endogenous conditions, revealing its physiological relevance. We identified several SUMO sites in eIF5A and found that SUMOylation modulates both the stability and the localization of eIF5A in mammalian cells. Interestingly, the SUMOylation of eIF5A responds to specific stresses, indicating that it is a regulated process. SUMOylation of eIF5A is conserved in yeast, the eIF5A SUMOylation mutants are unable to completely suppress the defects of HYP2 mutants, and SUMOylation of eIF5A is important for both stress granules formation and disassembly of polysomes induced by heat-shock. Moreover, mutation of the SUMOylation sites in eIF5A abolishes its promigratory and proproliferative activities in PANC-1 cells.
    Conclusions: SUMO2 conjugation to eIF5A is a stress-induced response implicated in the adaptation of yeast cells to heat-shock stress and required to promote the growth and migration of pancreatic ductal adenocarcinoma cells.
    MeSH term(s) Animals ; Humans ; Adenocarcinoma ; Mammals ; Proteomics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Small Ubiquitin-Related Modifier Proteins/genetics ; Small Ubiquitin-Related Modifier Proteins/metabolism ; Sumoylation ; Ubiquitin/metabolism
    Chemical Substances Small Ubiquitin-Related Modifier Proteins ; Ubiquitin ; eIF5A protein, S cerevisiae
    Language English
    Publishing date 2024-01-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2108724-6
    ISSN 1689-1392 ; 1689-1392
    ISSN (online) 1689-1392
    ISSN 1689-1392
    DOI 10.1186/s11658-024-00533-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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