BioID data of c-MYC interacting protein partners in cultured cells and xenograft tumors

Metallothionein 3 (MT-3), also known as growth inhibitory factor (GIF), exhibits a neuroinhibitory activity. Our lab and others have previously shown that this biological activity involves interacting protein partners in the brain. However, nothing specific is yet known about which of these interactions is responsible for the GIF activity. In this paper, we are reporting upon new proteins found interacting with MT-3 as determined through immunoaffinity chromatography and mass spectrometry. These new partner proteins—Exo84p, 14-3-3 Zeta,αandβEnolase, Aldolase C, Malate dehydrogenase, ATP synthase, and Pyruvate kinase—along with those previously identified have now been classified into three functional groups: transport and signaling, chaperoning and scaffolding, and glycolytic metabolism. When viewed together, these interactions support a proposed model for the regulation of the GIF activity of MT-3.

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The Many Faces of FKBP51

Biomolecules ◽

10.3390/biom9010035 ◽

2019 ◽

Vol 9 (1) ◽

pp. 35 ◽

Cited By ~ 18

Author(s):

Andreas Hähle ◽

Stephanie Merz ◽

Christian Meyners ◽

Felix Hausch

Keyword(s):

Stress Responses ◽

Molecular Mechanisms ◽

Post Traumatic Stress ◽

Interacting Protein ◽

Fk506 Binding Protein ◽

Obesity And Diabetes ◽

Protein Partners ◽

Interaction Partners ◽

Post Traumatic ◽

The Many

The FK506-binding protein 51 (FKBP51) has emerged as a key regulator of endocrine stress responses in mammals and as a potential therapeutic target for stress-related disorders (depression, post-traumatic stress disorder), metabolic disorders (obesity and diabetes) and chronic pain. Recently, FKBP51 has been implicated in several cellular pathways and numerous interacting protein partners have been reported. However, no consensus on the underlying molecular mechanisms has yet emerged. Here, we review the protein interaction partners reported for FKBP51, the proposed pathways involved, their relevance to FKBP51’s physiological function(s), the interplay with other FKBPs, and implications for the development of FKBP51-directed drugs.

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Rab9 GTPase Regulates Late Endosome Size and Requires Effector Interaction for Its Stability

Molecular Biology of the Cell ◽

10.1091/mbc.e04-08-0747 ◽

2004 ◽

Vol 15 (12) ◽

pp. 5420-5430 ◽

Cited By ~ 108

Author(s):

Ian G. Ganley ◽

Kate Carroll ◽

Lenka Bittova ◽

Suzanne Pfeffer

Keyword(s):

Membrane Protein ◽

Cultured Cells ◽

Late Endosome ◽

Interacting Protein ◽

Late Endosomes ◽

Specific Effector ◽

Mannose 6 Phosphate ◽

Endocytic Compartments ◽

Gdp Dissociation Inhibitor ◽

Multivesicular Endosomes

Rab9 GTPase resides in a late endosome microdomain together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kDa (TIP47). To explore the importance of Rab9 for microdomain establishment, we depleted the protein from cultured cells. Rab9 depletion decreased late endosome size and reduced the numbers of multilamellar and dense-tubule–containing late endosomes/lysosomes, but not multivesicular endosomes. The remaining late endosomes and lysosomes were more tightly clustered near the nucleus, implicating Rab9 in endosome localization. Cells displayed increased surface MPRs and lysosome-associated membrane protein 1. In addition, cells showed increased MPR synthesis in conjunction with MPR missorting to the lysosome. Surprisingly, Rab9 stability on late endosomes required interaction with TIP47. Rabs are thought of as independent, prenylated entities that reside either on membranes or in cytosol, bound to GDP dissociation inhibitor. These data show that Rab9 stability is strongly influenced by a specific effector interaction. Moreover, Rab9 and the proteins with which it interacts seem critical for the maintenance of specific late endocytic compartments and endosome/lysosome localization.

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Arabidopsis B-BOX32 interacts with CONSTANS-LIKE3 to regulate flowering

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1616459114 ◽

2016 ◽

Vol 114 (1) ◽

pp. 172-177 ◽

Cited By ~ 22

Author(s):

Prateek Tripathi ◽

Marcela Carvallo ◽

Elizabeth E. Hamilton ◽

Sasha Preuss ◽

Steve A. Kay

Keyword(s):

Large Scale ◽

Early Morning ◽

Day Length ◽

Interacting Protein ◽

Protein Partners ◽

Biochemical Assays ◽

Environmental Variations ◽

Developmental Switch ◽

Two Hybrid

Plants have the ability to respond to seasonal environmental variations by monitoring day length to initiate flowering. The transition from vegetative to the reproductive stage is the critical developmental switch in flowering plants to ensure optimal fitness and/or yield. It has been previously reported that B-BOX32 (BBX32) has the potential to increase grain yield when ectopically expressed in soybean. In the present study, we performed a detailed molecular characterization of the Arabidopsis B-box domain gene BBX32. We showed that the circadian clock in Arabidopsis regulates BBX32 and expressed in the early morning. To understand the molecular mechanism of BBX32 regulation, we performed a large-scale yeast two-hybrid screen and identified CONSTANS-LIKE 3 (COL3)/BBX4 as one of its interacting protein partners. Using different genetic and biochemical assays, we have validated this interaction and shown that COL3 targets FT in the presence of BBX32 to regulate the flowering pathway. Based on these findings, we hypothesized that this BBX32-COL3 module could be an additional regulatory mechanism affecting the reproductive development in Arabidopsis that could be translated to crops for increased agricultural productivity.

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The mammalian ULK1 complex and autophagy initiation

Essays in Biochemistry ◽

10.1042/ebc20170021 ◽

2017 ◽

Vol 61 (6) ◽

pp. 585-596 ◽

Cited By ~ 149

Author(s):

Maria Zachari ◽

Ian G. Ganley

Keyword(s):

Control Mechanism ◽

Degradation Pathway ◽

Autophagosome Formation ◽

Interacting Protein ◽

Initial Event ◽

Protein Partners ◽

Recycling Pathway ◽

Quality Control Mechanism ◽

Cellular Components ◽

Membrane Organelle

Autophagy is a vital lysosomal degradation pathway that serves as a quality control mechanism. It rids the cell of damaged, toxic or excess cellular components, which if left to persist could be detrimental to the cell. It also serves as a recycling pathway to maintain protein synthesis under starvation conditions. A key initial event in autophagy is formation of the autophagosome, a unique double-membrane organelle that engulfs the cytosolic cargo destined for degradation. This step is mediated by the serine/threonine protein kinase ULK1 (unc-51-like kinase 1), which functions in a complex with at least three protein partners: FIP200 (focal adhesion kinase family interacting protein of 200 kDa), ATG (autophagy-related protein) 13 (ATG13), and ATG101. In this artcile, we focus on the regulation of the ULK1 complex during autophagy initiation. The complex pattern of upstream pathways that converge on ULK1 suggests that this complex acts as a node, converting multiple signals into autophagosome formation. Here, we review our current understanding of this regulation and in turn discuss what happens downstream, once the ULK1 complex becomes activated.

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Glutamate Receptor Auxiliary Subunits and Interacting Protein Partners in the Cerebellum

10.1007/978-3-030-23810-0_35 ◽

2021 ◽

pp. 929-955

Author(s):

Ian D. Coombs ◽

Stuart G. Cull-Candy

Keyword(s):

Glutamate Receptor ◽

Interacting Protein ◽

Auxiliary Subunits ◽

Protein Partners

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The Methyl-CpG Binding Protein MBD1 Interacts with the p150 Subunit of Chromatin Assembly Factor 1

Molecular and Cellular Biology ◽

10.1128/mcb.23.9.3226-3236.2003 ◽

2003 ◽

Vol 23 (9) ◽

pp. 3226-3236 ◽

Cited By ~ 61

Author(s):

Brian E. Reese ◽

Kurtis E. Bachman ◽

Stephen B. Baylin ◽

Michael R. Rountree

Keyword(s):

Transcriptional Repression ◽

Histone Deacetylases ◽

Promoter Hypermethylation ◽

Chromatin Assembly ◽

Interacting Protein ◽

Chromatin Assembly Factor ◽

C Terminus ◽

Protein Partners ◽

Assembly Factor ◽

Heterochromatin Structure

ABSTRACT DNA promoter hypermethylation has been shown to be a functional mechanism of transcriptional repression. This epigenetic gene silencing is thought to involve the recruitment of chromatin-remodeling factors, such as histone deacetylases, to methylated DNA via a family of proteins called methyl-CpG binding proteins (MBD1 to -4). MBD1, a member of this family, exhibits transcription-repressive activity, but to this point no interacting protein partners have been identified. In this study, we demonstrate that MBD1 partners with the p150 subunit of chromatin assembly factor 1 (CAF-1), forming a multiprotein complex that also contains HP1α. The MBD1-CAF-1 p150 interaction requires the methyl-CpG binding domain of MBD1, and the association occurs in the C terminus of CAF-1 p150. The two proteins colocalize to regions of dense heterochromatin in mouse cells, and overexpression of the C terminus of CAF-1 p150 prevents the targeting of MBD1 in these cells without disrupting global heterochromatin structure. This interaction suggests a role for MBD1 and CAF-1 p150 in methylation-mediated transcriptional repression and the inheritance of epigenetically determined chromatin states.

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Ablation of RIP3 protects from dopaminergic neurodegeneration in experimental Parkinson’s disease

Cell Death and Disease ◽

10.1038/s41419-019-2078-z ◽

2019 ◽

Vol 10 (11) ◽

Cited By ~ 7

Author(s):

Pedro A. Dionísio ◽

Sara R. Oliveira ◽

Maria M. Gaspar ◽

Maria J. Gama ◽

Margarida Castro-Caldas ◽

...

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Cell Death ◽

Cultured Cells ◽

Substantia Nigra Pars Compacta ◽

Neuronal Cultures ◽

Interacting Protein ◽

Dopaminergic Neurodegeneration

Abstract Parkinson’s disease (PD) is driven by dopaminergic neurodegeneration in the substantia nigra pars compacta (SN) and striatum. Although apoptosis is considered the main neurodegenerative mechanism, other cell death pathways may be involved. In this regard, necroptosis is a regulated form of cell death dependent on receptor interacting protein 3 (RIP3), a protein also implicated in apoptosis and inflammation independently of its pro-necroptotic activity. Here, we explored the role of RIP3 genetic deletion in in vivo and in vitro PD models. Firstly, wild-type (Wt) and RIP3 knockout (RIP3ko) mice were injected intraperitoneally with MPTP (40 mg/kg, i.p.), and sacrificed after either 6 or 30 days. RIP3ko protected from dopaminergic neurodegeneration in the SN of MPTP-injected mice, but this effect was independent of necroptosis. In keeping with this, necrostatin-1s (10 mg/kg/day, i.p.) did not afford full neuroprotection. Moreover, MPTP led to DNA fragmentation, caspase-3 activation, lipid peroxidation and BAX expression in Wt mice, in the absence of caspase-8 cleavage, suggesting intrinsic apoptosis. This was mimicked in primary cortical neuronal cultures exposed to the active MPTP metabolite. RIP3 deficiency in cultured cells and in mouse brain abrogated all phenotypes. Curiously, astrogliosis was increased in the striatum of MPTP-injected Wt mice and further exacerbated in RIP3ko mice. This was accompanied by absence of microgliosis and reposition of glial cell line-derived neurotrophic factor (GDNF) levels in the striata of MPTP-injected RIP3ko mice when compared to MPTP-injected Wt mice, which in turn showed a massive GDNF decrease. RIP3ko primary mixed glial cultures also presented decreased expression of inflammation-related genes upon inflammatory stimulation. These findings hint at possible undescribed non-necroptotic roles for RIP3 in inflammation and MPTP-driven cell death, which can contribute to PD progression.

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