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Article ; Online: The Extent of Extended-Ubiquitin Binding to the Proteasome.

Roelofs, Jeroen

Structure (London, England : 1993)

2020 Volume 28, Issue 5, Page(s) 489–491

Abstract: In this issue of Structure, Lu et al. (2020) describe an NMR-based study showing the proteasome ubiquitin receptor hRpn13 bound to an extended conformation of K48-diubiquitin that is different from previously described structures of K48-diubiquitin. ... ...

Abstract	In this issue of Structure, Lu et al. (2020) describe an NMR-based study showing the proteasome ubiquitin receptor hRpn13 bound to an extended conformation of K48-diubiquitin that is different from previously described structures of K48-diubiquitin. Observed dynamic binding properties suggest an ability of substrates to hop between proteasome ubiquitin receptors.
MeSH term(s)	Molecular Conformation ; Proteasome Endopeptidase Complex ; Protein Binding ; Ubiquitin ; Ubiquitins
Chemical Substances	Ubiquitin ; Ubiquitins ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2020-05-31
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2020.04.013
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Article ; Online: Proteasome granule formation is regulated through mitochondrial respiration and kinase signaling.

Waite, Kenrick A / Roelofs, Jeroen

Journal of cell science

2022 Volume 135, Issue 17

Abstract: In the yeast Saccharomyces cerevisiae, proteasomes are enriched in cell nuclei, in which they execute important cellular functions. Nutrient stress can change this localization, indicating that proteasomes respond to the metabolic state of the cell. ... ...

Abstract	In the yeast Saccharomyces cerevisiae, proteasomes are enriched in cell nuclei, in which they execute important cellular functions. Nutrient stress can change this localization, indicating that proteasomes respond to the metabolic state of the cell. However, the signals that connect these processes remain poorly understood. Carbon starvation triggers a reversible translocation of proteasomes to cytosolic condensates known as proteasome storage granules. Surprisingly, we observed strongly reduced levels of proteasome granules when cells had active cellular respiration prior to starvation. This suggests that the mitochondrial activity of cells is a determining factor in the response of proteasomes to carbon starvation. Consistent with this, upon inhibition of mitochondrial function, we observed that proteasomes relocalize to granules. These links between proteasomes and metabolism involve specific signaling pathways, as we identified a mitogen-activated protein kinase (MAPK) cascade that is critical to the formation of proteasome granules after respiratory growth but not following glycolytic growth. Furthermore, the yeast homolog of AMP kinase, Snf1, is important for proteasome granule formation induced by mitochondrial inhibitors, but it is dispensable for granule formation following carbon starvation. We propose a model in which mitochondrial activity promotes nuclear localization of the proteasome. This article has an associated First Person interview with the first author of the paper.
MeSH term(s)	Carbon/metabolism ; Humans ; Mitochondria/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Respiration ; Saccharomyces cerevisiae/metabolism
Chemical Substances	Carbon (7440-44-0) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2022-09-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.259778
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Article ; Online: Proteasome condensate formation is driven by multivalent interactions with shuttle factors and ubiquitin chains.

Waite, Kenrick A / Vontz, Gabrielle / Lee, Stella Y / Roelofs, Jeroen

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

2024 Volume 121, Issue 10, Page(s) e2310756121

Abstract: Stress conditions can cause the relocalization of proteasomes to condensates in yeast and mammalian cells. The interactions that facilitate the formation of proteasome condensates, however, are unclear. Here, we show that the formation of proteasome ... ...

Abstract	Stress conditions can cause the relocalization of proteasomes to condensates in yeast and mammalian cells. The interactions that facilitate the formation of proteasome condensates, however, are unclear. Here, we show that the formation of proteasome condensates in yeast depends on ubiquitin chains together with the proteasome shuttle factors Rad23 and Dsk2. These shuttle factors colocalize to these condensates. Strains deleted for the third shuttle factor gene,
MeSH term(s)	Animals ; Ubiquitin/genetics ; Proteasome Endopeptidase Complex/genetics ; Proteasome Endopeptidase Complex/chemistry ; Saccharomyces cerevisiae/genetics ; Ubiquitins/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/chemistry ; Cell Cycle Proteins/genetics ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/chemistry ; Mammals
Chemical Substances	Ubiquitin ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Ubiquitins ; Saccharomyces cerevisiae Proteins ; Cell Cycle Proteins ; DNA-Binding Proteins
Language	English
Publishing date	2024-02-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2310756121
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Article: Proteasome condensate formation is driven by multivalent interactions with shuttle factors and K48-linked ubiquitin chains.

Waite, Kenrick A / Vontz, Gabrielle / Lee, Stella Y / Roelofs, Jeroen

bioRxiv : the preprint server for biology

2023

Abstract	Stress conditions can cause the relocalization of proteasomes to condensates in yeast and mammalian cells. The interactions that facilitate the formation of proteasome condensates, however, are unclear. Here, we show that the formation of proteasome condensates in yeast depends on long K48-linked ubiquitin chains together with the proteasome shuttle factors Rad23 and Dsk2. These shuttle factors colocalize to these condensates. Strains deleted for the third shuttle factor gene, Significance: Stress conditions can cause the relocalization of proteasomes to condensates in yeast as well as mammalian cells. Our work shows that the formation of proteasome condensates in yeast depends on long K48-linked ubiquitin chains, the proteasome binding shuttle factors Rad23 and Dsk2 and proteasome intrinsic ubiquitin receptors. Here, different receptors are critical for different condensate inducers. These results indicate distinct condensates can form with specific functionality. Our identification of key factors involved in the process is crucial for understanding the function of proteasome relocalization to condensates. We propose that cellular accumulation of substrates with long ubiquitin chains results in the formation of condensates comprising those ubiquitinated substrates, proteasomes, and proteasome shuttle factors, where the ubiquitin chains serve as the scaffold for condensate formation.
Language	English
Publishing date	2023-06-26
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.25.546446
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Article: Proteasome inhibition by bortezomib: A left hook and a right punch.

Roelofs, Jeroen

EBioMedicine

2015 Volume 2, Issue 7, Page(s) 619–620

MeSH term(s)	Bortezomib/pharmacology ; Humans ; Intracellular Space/enzymology ; Proteasome Endopeptidase Complex/chemistry ; Proteasome Endopeptidase Complex/metabolism
Chemical Substances	Bortezomib (69G8BD63PP) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2015-07
Publishing country	Netherlands
Document type	Comment ; Journal Article
ZDB-ID	2851331-9
ISSN	2352-3964 ; 2352-3964
ISSN (online)	2352-3964
ISSN	2352-3964
DOI	10.1016/j.ebiom.2015.07.009
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Article ; Online: Tagging the proteasome active site β5 causes tag specific phenotypes in yeast.

Waite, Kenrick A / Burris, Alicia / Roelofs, Jeroen

Scientific reports

2020 Volume 10, Issue 1, Page(s) 18133

Abstract: The efficient and timely degradation of proteins is crucial for many cellular processes and to maintain general proteostasis. The proteasome, a complex multisubunit protease, plays a critical role in protein degradation. Therefore, it is important to ... ...

Abstract	The efficient and timely degradation of proteins is crucial for many cellular processes and to maintain general proteostasis. The proteasome, a complex multisubunit protease, plays a critical role in protein degradation. Therefore, it is important to understand the assembly, regulation, and localization of proteasome complexes in the cell under different conditions. Fluorescent tags are often utilized to study proteasomes. A GFP-tag on the β5 subunit, one of the core particle (CP) subunits with catalytic activity, has been shown to be incorporated into proteasomes and commonly used by the field. We report here that a tag on this subunit results in aberrant phenotypes that are not observed when several other CP subunits are tagged. These phenotypes appear in combination with other proteasome mutations and include poor growth, and, more significantly, altered 26S proteasome localization. In strains defective for autophagy, β5-GFP tagged proteasomes, unlike other CP tags, localize to granules upon nitrogen starvation. These granules are reflective of previously described proteasome storage granules but display unique properties. This suggests proteasomes with a β5-GFP tag are specifically recognized and sequestered depending on physiological conditions. In all, our data indicate the intricacy of tagging proteasomes, and possibly, large complexes in general.
MeSH term(s)	Catalytic Domain ; Green Fluorescent Proteins/metabolism ; Phenotype ; Proteasome Endopeptidase Complex/metabolism ; Protein Subunits ; Proteostasis ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/growth & development ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Protein Subunits ; Saccharomyces cerevisiae Proteins ; Green Fluorescent Proteins (147336-22-9) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2020-10-22
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-75126-1
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Article ; Online: Proteaphagy is specifically regulated and requires factors dispensable for general autophagy.

Waite, Kenrick A / Burris, Alicia / Vontz, Gabrielle / Lang, Angelica / Roelofs, Jeroen

The Journal of biological chemistry

2021 Volume 298, Issue 1, Page(s) 101494

Abstract: Changing physiological conditions can increase the need for protein degradative capacity in eukaryotic cells. Both the ubiquitin-proteasome system and autophagy contribute to protein degradation. However, these processes can be differently regulated ... ...

Abstract	Changing physiological conditions can increase the need for protein degradative capacity in eukaryotic cells. Both the ubiquitin-proteasome system and autophagy contribute to protein degradation. However, these processes can be differently regulated depending on the physiological conditions. Strikingly, proteasomes themselves can be a substrate for autophagy. The signals and molecular mechanisms that govern proteasome autophagy (proteaphagy) are only partly understood. Here, we used immunoblots, native gel analyses, and fluorescent microscopy to understand the regulation of proteaphagy in response to genetic and small molecule-induced perturbations. Our data indicate that chemical inhibition of the master nutrient sensor TORC1 (inhibition of which induces general autophagy) with rapamycin induces a bi-phasic response where proteasome levels are upregulated after an autophagy-dependent reduction. Surprisingly, several conditions that result in inhibited TORC1, such as caffeinine treatment or nitrogen starvation, only induced proteaphagy (i.e., without any proteasome upregulation), suggesting a convergence of signals upstream of proteaphagy under different physiological conditions. Indeed, we found that several conditions that activated general autophagy did not induce proteaphagy, further distinguishing proteaphagy from general autophagy. Consistent with this, we show that Atg11, a selective autophagy receptor, as well as the MAP kinases Mpk1, Mkk1, and Mkk2 all play a role in autophagy of proteasomes, although they are dispensable for general autophagy. Taken together, our data provide new insights into the molecular regulation of proteaphagy by demonstrating that degradation of proteasome complexes is specifically regulated under different autophagy-inducing conditions.
MeSH term(s)	Autophagy/physiology ; Macroautophagy ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Ubiquitination
Chemical Substances	Mechanistic Target of Rapamycin Complex 1 (EC 2.7.11.1) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2021-12-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; 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.2021.101494
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Article ; Online: Proteasome activator Blm10 levels and autophagic degradation directly impact the proteasome landscape.

Burris, Alicia / Waite, Kenrick A / Reuter, Zachary / Ockerhausen, Samuel / Roelofs, Jeroen

The Journal of biological chemistry

2021 Volume 296, Page(s) 100468

Abstract: The proteasome selectively degrades proteins. It consists of a core particle (CP), which contains proteolytic active sites that can associate with different regulators to form various complexes. How these different complexes are regulated and affected by ...

Abstract	The proteasome selectively degrades proteins. It consists of a core particle (CP), which contains proteolytic active sites that can associate with different regulators to form various complexes. How these different complexes are regulated and affected by changing physiological conditions, however, remains poorly understood. In this study, we focused on the activator Blm10 and the regulatory particle (RP). In yeast, increased expression of Blm10 outcompeted RP for CP binding, which suggests that controlling the cellular levels of Blm10 can affect the relative amounts of RP-bound CP. While strong overexpression of BLM10 almost eliminated the presence of RP-CP complexes, the phenotypes this should induce were not observed. Our results show this was due to the induction of Blm10-CP autophagy under prolonged growth in YPD. Similarly, under conditions of endogenous BLM10 expression, Blm10 was degraded through autophagy as well. This suggests that reducing the levels of Blm10 allows for more CP-binding surfaces and the formation of RP-CP complexes under nutrient stress. This work provides important insights into maintaining the proteasome landscape and how protein expression levels affect proteasome function.
MeSH term(s)	Autophagy/genetics ; Autophagy/physiology ; Cytoplasm ; Proteasome Endopeptidase Complex/genetics ; Proteasome Endopeptidase Complex/metabolism ; Protein Processing, Post-Translational ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Blm10 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2021-02-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2021.100468
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Article ; Online: Native Gel Approaches in Studying Proteasome Assembly and Chaperones.

Roelofs, Jeroen / Suppahia, Anjana / Waite, Kenrick A / Park, Soyeon

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

2018 Volume 1844, Page(s) 237–260

Abstract: Proteasomes are complex molecular machines that consist of 66 subunits. The assembly of these complexes is highly coordinated in a process that requires at least ten proteasome-specific molecular chaperones. One of the challenges in studying assembly ... ...

Abstract	Proteasomes are complex molecular machines that consist of 66 subunits. The assembly of these complexes is highly coordinated in a process that requires at least ten proteasome-specific molecular chaperones. One of the challenges in studying assembly intermediates is their relatively low abundance as compared to the proteasome holoenzyme. Therefore, superior separating techniques are crucial for analyses of proteasomal complexes in general and studies in the assembly in particular. For this reason, native gel analyses have been abundantly used in studying proteasomes, as they provide a high resolution. Native gels are very versatile and can be used in various combinatorial approaches. In this chapter, we outline two approaches to prepare samples for native gels. The first is a yeast cryogrinding method and the second a core particle (CP)-base reconstitution approach. We describe the native gel electrophoresis, as well as various downstream analyses, including 2D native-SDS-PAGE. These techniques and approaches can all be used, often in parallel, to gain a variety of information about activity and composition of the complexes separated by native gel. The potential combined approaches are discussed in this review.
MeSH term(s)	Electrophoresis, Gel, Two-Dimensional/methods ; Fungal Proteins ; Molecular Chaperones/chemistry ; Molecular Chaperones/metabolism ; Native Polyacrylamide Gel Electrophoresis ; Proteasome Endopeptidase Complex/chemistry ; Proteasome Endopeptidase Complex/metabolism ; Recombinant Proteins/chemistry ; Recombinant Proteins/metabolism ; Yeasts/metabolism
Chemical Substances	Fungal Proteins ; Molecular Chaperones ; Recombinant Proteins ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2018-09-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8706-1_16
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Article ; Online: A retrospective survey of the causes of bracket- and tube-bonding failures.

Roelofs, Tom / Merkens, Nico / Roelofs, Jeroen / Bronkhorst, Ewald / Breuning, Hero

The Angle orthodontist

2016 Volume 87, Issue 1, Page(s) 111–117

Abstract: Objective: To investigate the causes of bonding failures of orthodontic brackets and tubes and the effect of premedicating for saliva reduction.: Materials and methods: Premedication with atropine sulfate was administered randomly. Failure rate of ... ...

Abstract	Objective: To investigate the causes of bonding failures of orthodontic brackets and tubes and the effect of premedicating for saliva reduction. Materials and methods: Premedication with atropine sulfate was administered randomly. Failure rate of brackets and tubes placed in a group of 158 consecutive patients was evaluated after a mean period of 67 weeks after bonding. Results: The failure rate in the group without atropine sulfate premedication was 2.4%. In the group with premedication, the failure rate was 2.7%. The Cox regression analysis of these groups showed that atropine application did not lead to a reduction in bond failures. Statistically significant differences in the hazard ratio were found for the bracket regions and for the dental assistants who prepared for the bonding procedure. Conclusions: Premedication did not lead to fewer bracket failures. The roles of the dental assistant and patient in preventing failures was relevant. A significantly higher failure rate for orthodontic appliances was found in the posterior regions.
MeSH term(s)	Adolescent ; Adult ; Atropine ; Bicuspid ; Child ; Child, Preschool ; Dental Bonding/methods ; Dental Bonding/statistics & numerical data ; Equipment Failure ; Female ; Humans ; Kaplan-Meier Estimate ; Male ; Molar ; Orthodontic Appliances ; Orthodontic Brackets ; Proportional Hazards Models ; Retrospective Studies ; Saliva ; Salivation ; Stainless Steel/chemistry ; Surveys and Questionnaires ; Test Taking Skills ; Young Adult
Chemical Substances	Stainless Steel (12597-68-1) ; Atropine (7C0697DR9I)
Language	English
Publishing date	2016-06-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	390289-4
ISSN	1945-7103 ; 0003-3219
ISSN (online)	1945-7103
ISSN	0003-3219
DOI	10.2319/021616-136.1
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