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  1. Article ; Online: Ubiquitination of non-protein substrates.

    Sakamaki, Jun-Ichi / Mizushima, Noboru

    Trends in cell biology

    2023  Volume 33, Issue 11, Page(s) 991–1003

    Abstract: The covalent attachment of ubiquitin is a common regulatory mechanism in various proteins. Although it has long been thought that the substrates of ubiquitination are limited to proteins, recent studies have changed this view: ubiquitin can be conjugated ...

    Abstract The covalent attachment of ubiquitin is a common regulatory mechanism in various proteins. Although it has long been thought that the substrates of ubiquitination are limited to proteins, recent studies have changed this view: ubiquitin can be conjugated to lipids, sugars, and nucleotides. Ubiquitin is linked to these substrates by the action of different classes of ubiquitin ligases that have distinct catalytic mechanisms. Ubiquitination of non-protein substrates likely serves as a signal for the recruitment of other proteins to bring about specific effects. These discoveries have expanded the concept of ubiquitination and have advanced our insight into the biology and chemistry of this well-established modification process. In this review we describe the molecular mechanisms and roles of non-protein ubiquitination and discuss the current limitations.
    Language English
    Publishing date 2023-04-27
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 30122-x
    ISSN 1879-3088 ; 0962-8924
    ISSN (online) 1879-3088
    ISSN 0962-8924
    DOI 10.1016/j.tcb.2023.03.014
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  2. Article ; Online: Cell biology of protein-lipid conjugation.

    Sakamaki, Jun-Ichi / Mizushima, Noboru

    Cell structure and function

    2023  Volume 48, Issue 1, Page(s) 99–112

    Abstract: Protein-lipid conjugation is a widespread modification involved in many biological processes. Various lipids, including fatty acids, isoprenoids, sterols, glycosylphosphatidylinositol, sphingolipids, and phospholipids, are covalently linked with proteins. ...

    Abstract Protein-lipid conjugation is a widespread modification involved in many biological processes. Various lipids, including fatty acids, isoprenoids, sterols, glycosylphosphatidylinositol, sphingolipids, and phospholipids, are covalently linked with proteins. These modifications direct proteins to intracellular membranes through the hydrophobic nature of lipids. Some of these membrane-binding processes are reversible through delipidation or by reducing the affinity to membranes. Many signaling molecules undergo lipid modification, and their membrane binding is important for proper signal transduction. The conjugation of proteins to lipids also influences the dynamics and function of organellar membranes. Dysregulation of lipidation has been associated with diseases such as neurodegenerative diseases. In this review, we first provide an overview of diverse forms of protein-lipid conjugation and then summarize the catalytic mechanisms, regulation, and roles of these modifications.Key words: lipid, lipidation, membrane, organelle, protein modification.
    MeSH term(s) Proteins ; Fatty Acids/metabolism ; Phospholipids/metabolism ; Lipid Metabolism ; Sterols/metabolism ; Cell Membrane/metabolism
    Chemical Substances Proteins ; Fatty Acids ; Phospholipids ; Sterols
    Language English
    Publishing date 2023-04-06
    Publishing country Japan
    Document type Review ; Journal Article
    ZDB-ID 197293-5
    ISSN 1347-3700 ; 0386-7196
    ISSN (online) 1347-3700
    ISSN 0386-7196
    DOI 10.1247/csf.23016
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  3. Article ; Online: Protocol to purify and detect ubiquitinated phospholipids in budding yeast and human cell lines

    Jun-ichi Sakamaki / Noboru Mizushima

    STAR Protocols, Vol 4, Iss 1, Pp 101935- (2023)

    1480  

    Abstract: ... execution of this protocol, please refer to Sakamaki et al.1 : Publisher’s note: Undertaking ...

    Abstract Summary: Ubiquitin is covalently conjugated to phospholipids as well as proteins; however, ubiquitinated phospholipids are less abundant than free ubiquitin and ubiquitinated proteins. Here, we describe protocols to purify ubiquitinated phospholipids in budding yeast and human cells based on their hydrophobicity. Ubiquitinated phospholipids are purified by Triton X-114 phase partitioning and affinity purification and verified by phospholipase D treatment. These protocols enable the detection of tagged as well as endogenous mono- and poly-ubiquitinated phospholipids by immunoblotting.For complete details on the use and execution of this protocol, please refer to Sakamaki et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
    Keywords Cell Biology ; Model Organisms ; Molecular Biology ; Protein Biochemistry ; Science (General) ; Q1-390
    Subject code 500
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Cell biology of protein–lipid conjugation

    Jun-ichi Sakamaki / Noboru Mizushima

    Cell Structure and Function, Vol 48, Iss 1, Pp 99-

    2023  Volume 112

    Abstract: Protein–lipid conjugation is a widespread modification involved in many biological processes. Various lipids, including fatty acids, isoprenoids, sterols, glycosylphosphatidylinositol, sphingolipids, and phospholipids, are covalently linked with proteins. ...

    Abstract Protein–lipid conjugation is a widespread modification involved in many biological processes. Various lipids, including fatty acids, isoprenoids, sterols, glycosylphosphatidylinositol, sphingolipids, and phospholipids, are covalently linked with proteins. These modifications direct proteins to intracellular membranes through the hydrophobic nature of lipids. Some of these membrane-binding processes are reversible through delipidation or by reducing the affinity to membranes. Many signaling molecules undergo lipid modification, and their membrane binding is important for proper signal transduction. The conjugation of proteins to lipids also influences the dynamics and function of organellar membranes. Dysregulation of lipidation has been associated with diseases such as neurodegenerative diseases. In this review, we first provide an overview of diverse forms of protein–lipid conjugation and then summarize the catalytic mechanisms, regulation, and roles of these modifications. Key words: lipid, lipidation, membrane, organelle, protein modification
    Keywords lipid ; lipidation ; membrane ; organelle ; protein modification ; Science ; Q ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Japan Society of Cell Biology
    Document type Article ; Online
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  5. Article ; Online: Protocol to purify and detect ubiquitinated phospholipids in budding yeast and human cell lines.

    Sakamaki, Jun-Ichi / Mizushima, Noboru

    STAR protocols

    2022  Volume 4, Issue 1, Page(s) 101935

    Abstract: ... execution of this protocol, please refer to Sakamaki et al.. ...

    Abstract Ubiquitin is covalently conjugated to phospholipids as well as proteins; however, ubiquitinated phospholipids are less abundant than free ubiquitin and ubiquitinated proteins. Here, we describe protocols to purify ubiquitinated phospholipids in budding yeast and human cells based on their hydrophobicity. Ubiquitinated phospholipids are purified by Triton X-114 phase partitioning and affinity purification and verified by phospholipase D treatment. These protocols enable the detection of tagged as well as endogenous mono- and poly-ubiquitinated phospholipids by immunoblotting. For complete details on the use and execution of this protocol, please refer to Sakamaki et al..
    MeSH term(s) Humans ; Saccharomycetales/metabolism ; Ubiquitin/metabolism ; Proteins ; Immunoblotting ; Cell Line
    Chemical Substances Ubiquitin ; Proteins
    Language English
    Publishing date 2022-12-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2022.101935
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  6. Article ; Online: Conjugation of the ubiquitin family proteins to phospholipids.

    Sakamaki, Jun-Ichi / Mizushima, Noboru

    Autophagy

    2022  Volume 19, Issue 4, Page(s) 1361–1362

    Abstract: Conjugation of Atg8-family proteins to phosphatidylethanolamine (PE) is important for autophagosome formation. PE conjugation has been thought to be specific to Atg8 among the ubiquitin-family proteins. However, this dogma has not been experimentally ... ...

    Abstract Conjugation of Atg8-family proteins to phosphatidylethanolamine (PE) is important for autophagosome formation. PE conjugation has been thought to be specific to Atg8 among the ubiquitin-family proteins. However, this dogma has not been experimentally verified. Our recent study revealed that ubiquitin is also conjugated to PE on endosomes and the vacuole (or lysosomes). Other ubiquitin-like proteins, such as NEDD8 and ISG15, also covalently bind to phospholipids. We propose that conjugation to phospholipids could be a common feature of the ubiquitin family.
    MeSH term(s) Phospholipids ; Saccharomyces cerevisiae Proteins/metabolism ; Autophagy ; Autophagy-Related Protein 8 Family ; Ubiquitins ; Ubiquitin/metabolism ; Microtubule-Associated Proteins/metabolism ; Autophagy-Related Proteins
    Chemical Substances Phospholipids ; Saccharomyces cerevisiae Proteins ; Autophagy-Related Protein 8 Family ; Ubiquitins ; Ubiquitin ; Microtubule-Associated Proteins ; Autophagy-Related Proteins
    Language English
    Publishing date 2022-09-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2454135-7
    ISSN 1554-8635 ; 1554-8627
    ISSN (online) 1554-8635
    ISSN 1554-8627
    DOI 10.1080/15548627.2022.2123637
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  7. Article ; Online: The pH-sensing Rim101 pathway regulates cell size in budding yeast.

    Shimasawa, Masaru / Sakamaki, Jun-Ichi / Maeda, Tatsuya / Mizushima, Noboru

    The Journal of biological chemistry

    2023  Volume 299, Issue 3, Page(s) 102973

    Abstract: Although cell size regulation is crucial for cellular functions in a variety of organisms from bacteria to humans, the underlying mechanisms remain elusive. Here, we identify Rim21, a component of the pH-sensing Rim101 pathway, as a positive regulator of ...

    Abstract Although cell size regulation is crucial for cellular functions in a variety of organisms from bacteria to humans, the underlying mechanisms remain elusive. Here, we identify Rim21, a component of the pH-sensing Rim101 pathway, as a positive regulator of cell size through a flow cytometry-based genome-wide screen of Saccharomyces cerevisiae deletion mutants. We found that mutants defective in the Rim101 pathway were consistently smaller than wildtype cells in the log and stationary phases. We show that the expression of the active form of Rim101 increased the size of wildtype cells. Furthermore, the size of wildtype cells increased in response to external alkalization. Microscopic observation revealed that this cell size increase was associated with changes in both vacuolar and cytoplasmic volume. We also found that these volume changes were dependent on Rim21 and Rim101. In addition, a mutant lacking Vph1, a component of V-ATPase that is transcriptionally regulated by Rim101, was also smaller than wildtype cells, with no increase in size in response to alkalization. We demonstrate that the loss of Vph1 suppressed the Rim101-induced increase in cell size under physiological pH conditions. Taken together, our results suggest that the cell size of budding yeast is regulated by the Rim101-V-ATPase axis under physiological conditions as well as in response to alkaline stresses.
    MeSH term(s) Hydrogen-Ion Concentration ; Repressor Proteins/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Vacuolar Proton-Translocating ATPases/metabolism ; Sequence Deletion
    Chemical Substances Repressor Proteins ; RIM101 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; Vacuolar Proton-Translocating ATPases (EC 3.6.1.-)
    Language English
    Publishing date 2023-02-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2023.102973
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  8. Article ; Online: Ubiquitination of phosphatidylethanolamine in organellar membranes.

    Sakamaki, Jun-Ichi / Ode, Koji L / Kurikawa, Yoshitaka / Ueda, Hiroki R / Yamamoto, Hayashi / Mizushima, Noboru

    Molecular cell

    2022  Volume 82, Issue 19, Page(s) 3677–3692.e11

    Abstract: The covalent conjugation of ubiquitin family proteins is a widespread post-translational protein modification. In the ubiquitin family, the ATG8 subfamily is exceptional because it is conjugated mainly to phospholipids. However, it remains unknown ... ...

    Abstract The covalent conjugation of ubiquitin family proteins is a widespread post-translational protein modification. In the ubiquitin family, the ATG8 subfamily is exceptional because it is conjugated mainly to phospholipids. However, it remains unknown whether other ubiquitin family proteins are also conjugated to phospholipids. Here, we report that ubiquitin is conjugated to phospholipids, mainly phosphatidylethanolamine (PE), in yeast and mammalian cells. Ubiquitinated PE (Ub-PE) accumulates at endosomes and the vacuole (or lysosomes), and its level increases during starvation. Ub-PE is also found in baculoviruses. In yeast, PE ubiquitination is catalyzed by the canonical ubiquitin system enzymes Uba1 (E1), Ubc4/5 (E2), and Tul1 (E3) and is reversed by Doa4. Liposomes containing Ub-PE recruit the ESCRT components Vps27-Hse1 and Vps23 in vitro. Ubiquitin-like NEDD8 and ISG15 are also conjugated to phospholipids. These findings suggest that the conjugation to membrane phospholipids is not specific to ATG8 but is a general feature of the ubiquitin family.
    MeSH term(s) Animals ; Endosomal Sorting Complexes Required for Transport/genetics ; Endosomal Sorting Complexes Required for Transport/metabolism ; Liposomes/metabolism ; Mammals/metabolism ; Phosphatidylethanolamines/metabolism ; Phospholipids/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Ubiquitin/metabolism ; Ubiquitin-Conjugating Enzymes/genetics ; Ubiquitin-Conjugating Enzymes/metabolism ; Ubiquitination
    Chemical Substances Endosomal Sorting Complexes Required for Transport ; Hse1 protein, S cerevisiae ; Liposomes ; Phosphatidylethanolamines ; Phospholipids ; Receptors, Cytoplasmic and Nuclear ; Saccharomyces cerevisiae Proteins ; Ubiquitin ; VPS27 protein, S cerevisiae ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23)
    Language English
    Publishing date 2022-08-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2022.08.008
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  9. Article ; Online: Transcriptional regulation of autophagy and lysosomal function by bromodomain protein BRD4.

    Sakamaki, Jun-Ichi / Ryan, Kevin M

    Autophagy

    2017  Volume 13, Issue 11, Page(s) 2006–2007

    Abstract: Macroautophagy/autophagy is an intracellular recycling system that delivers cytoplasmic organelles and materials to lysosomes for degradation. This process is operated by autophagy-related (ATG) genes and tightly controlled by stress-responsive signaling ...

    Abstract Macroautophagy/autophagy is an intracellular recycling system that delivers cytoplasmic organelles and materials to lysosomes for degradation. This process is operated by autophagy-related (ATG) genes and tightly controlled by stress-responsive signaling pathways. Our recent study revealed that autophagy programs are transcriptionally suppressed by the BET family protein BRD4. This repression is alleviated during nutrient deprivation through the AMPK-SIRT1 pathway. Our findings therefore provide new insights into the regulation of autophagy.
    MeSH term(s) Autophagy ; Gene Expression Regulation ; Lysosomes ; Nuclear Proteins/genetics ; Transcription Factors/genetics
    Chemical Substances Nuclear Proteins ; Transcription Factors
    Language English
    Publishing date 2017-09-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2454135-7
    ISSN 1554-8635 ; 1554-8627
    ISSN (online) 1554-8635
    ISSN 1554-8627
    DOI 10.1080/15548627.2017.1364822
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  10. Article ; Online: Autophagy Determines the Path on the TRAIL to Death.

    Sakamaki, Jun-Ichi / Ryan, Kevin M

    Developmental cell

    2016  Volume 37, Issue 4, Page(s) 291–293

    Abstract: Macroautophagy facilitates degradation of cellular constituents and can positively or negatively affect cell death depending on the context. In this issue of Developmental Cell, Goodall and colleagues (2016) add to this complexity by showing that ... ...

    Abstract Macroautophagy facilitates degradation of cellular constituents and can positively or negatively affect cell death depending on the context. In this issue of Developmental Cell, Goodall and colleagues (2016) add to this complexity by showing that autophagy regulators can determine not only cell viability, but also the mechanism by which cells die.
    MeSH term(s) Animals ; Apoptosis/drug effects ; Autophagosomes/metabolism ; Autophagy/drug effects ; Humans ; Models, Biological ; Necrosis ; Signal Transduction ; TNF-Related Apoptosis-Inducing Ligand/pharmacology
    Chemical Substances TNF-Related Apoptosis-Inducing Ligand
    Language English
    Publishing date 2016-05-23
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2016.05.010
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