Protein misfolding specifies recruitment to cytoplasmic inclusion bodies

Bersuker, Kirill; Brandeis, Michael; Kopito, Ron R.

doi:10.1083/jcb.201511024

Cited by 35 publications

(34 citation statements)

References 71 publications

(97 reference statements)

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“…The YFP-UbiΔG75,76 mutant does not accumulate on aggregates. Moreover inhibition of ubiquitination by an E1 inhibitor [43] also prevented accumulation of ubiquitin on aggregates ([44] and data not shown). These observations indicate that aggregates don’t recruit free ubiquitin but only one conjugated to other proteins.…”

Section: Resultsmentioning

confidence: 97%

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Ubiquitin Accumulation on Disease Associated Protein Aggregates Is Correlated with Nuclear Ubiquitin Depletion, Histone De-Ubiquitination and Impaired DNA Damage Response

et al. 2017

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Deposition of ubiquitin conjugates on inclusion bodies composed of protein aggregates is a definitive cytopathological hallmark of neurodegenerative diseases. We show that accumulation of ubiquitin on polyQ IB, associated with Huntington’s disease, is correlated with extensive depletion of nuclear ubiquitin and histone de-ubiquitination. Histone ubiquitination plays major roles in chromatin regulation and DNA repair. Accordingly, we observe that cells expressing IB fail to respond to radiomimetic DNA damage, to induce gamma-H2AX phosphorylation and to recruit 53BP1 to damaged foci. Interestingly ubiquitin depletion, histone de-ubiquitination and impaired DNA damage response are not restricted to PolyQ aggregates and are associated with artificial aggregating luciferase mutants. The longevity of brain neurons depends on their capacity to respond to and repair extensive ongoing DNA damage. Impaired DNA damage response, even modest one, could thus lead to premature neuron aging and mortality.

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Section: Resultsmentioning

confidence: 97%

“…The initial trigger could be a small amount of ubiquitin on the primary aggregating protein or of co-aggregating proteins. We have recently shown that ubiquitin binds tightly to IB so that once it has been bound it remains there [44]. …”

Section: Discussionmentioning

confidence: 99%

Ubiquitin Accumulation on Disease Associated Protein Aggregates Is Correlated with Nuclear Ubiquitin Depletion, Histone De-Ubiquitination and Impaired DNA Damage Response

et al. 2017

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“…The screen identified two chemicals that blocked the increased abundance of NELFE at chromatin during heat shock: cycloheximide, an inhibitor of protein translation, and NSC 624206 (ref. 24 ), an inhibitor of ubiquitin E1 ligase (Ub-E1) ( Supplementary Fig. 5g).…”

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Nascent-protein ubiquitination is required for heat shock–induced gene downregulation in human cells

Aprile-Garcia

Tomar

Hummel

et al. 2019

Nat Struct Mol Biol

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hen eukaryotic cells are exposed to environmental stress, they mount an adaptive, conserved and coordinated response at the levels of transcription, translation, cell cycle and metabolism. The transcriptional response called the heat-shock response is typified by upregulation of heat-shock proteins or chaperones driven by the transcription factor heatshock factor (HSF) 1. Initially identified using heat-shock stress, the conserved HSF-driven response is now known to be induced by a variety of cellular conditions 2. Clinical studies have highlighted the relevance of the heat-shock response in cancer and neurodegeneration 3,4. Early studies have shown that stress such as heat shock not only upregulates chaperone genes, but also causes transcriptional downregulation of a handful of genes tested 5,6. Recent genome-wide technologies have confirmed a critical aspect of the heat-shock response: transcriptional downregulation of many highly expressed genes involved in metabolism, protein synthesis and cell cycle 7,8. Stress-induced transcriptional attenuation (SITA) is a rapid process conserved across Drosophila melanogaster 9 , mouse 7 and human cells 10. By downregulating the transcription of key genes, cells probably shift their resources from growth-promoting anabolic activities to dealing with proteotoxic stress. Despite the importance and conserved nature of SITA, relatively little is known about its underlying mechanistic basis. Two key questions need to be addressed: first, how are the rapid and reversible changes in transcription achieved at a molecular level; and second, how is the stress of heat shock sensed and communicated to transcriptional effectors? The primary stress sensor for chaperone upregulation, HSF, is not required for SITA 7 , suggesting an HSF-independent mechanism of stress sensing. How this mechanism is integrated with cellular stress response pathways is not understood. Metazoan transcription proceeds through two highly regulated steps 11,12. First, recruitment of RNA polymerase II (RNA Pol II) to core promoters leads to formation of a pre-initiation complex that transcribes about 20-60 bases downstream of transcription start sites (TSSs) and pauses. Sequence-specific transcription factors along with general transcription factors orchestrate this step. Second, release of promoter-proximal-paused RNA Pol II into productive elongation enables generation of a full-length transcript. Interplay between positive and negative transcription elongation factors (P-TEFs and N-TEFs, respectively) determines the fate of paused RNA Pol II, which is either termination followed by dissociation from promoters or transition to its elongating form. N-TEFs comprise several complexes including negative elongation factor (NELF), DRB-sensitivity inducing factor (DSIF), Integrator, tripartite motif containing 28 (TRIM28) and polymerase-associated factor 1 (PAF1) 13-16. N-TEFs oppose the elongation activity of P-TEFb, which consists of cyclin-dependent kinase 9 (Cdk9) and cyclin T 17. How stress affects the activity ...

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“…Upon acute removal of S1 from the culture medium ("washout" (w/o)), both proteins unfold, sampling different conformations and potentially transitioning dynamically among them (9,11). These partially unfolded proteins are targeted for ubiquitylation and, in the case of DD, rapid proteasomal degradation (t1 ⁄ 2 ϭ 90 min) (12,13). By contrast, S1 w/o causes AgDD to rapidly aggregate into puncta that are refractory to degradation and coalesce into cytoplasmic IBs (9).…”

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confidence: 99%

Acute unfolding of a single protein immediately stimulates recruitment of ubiquitin protein ligase E3C (UBE3C) to 26S proteasomes

Gottlieb

Thompson

Ordureau

et al. 2019

Journal of Biological Chemistry

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The intracellular accumulation of aggregated misfolded proteins is a cytopathological hallmark of neurodegenerative diseases. However, the functional relationship between protein misfolding or aggregation and the cellular proteostasis network that monitors and maintains proteome health is poorly understood. Previous studies have associated translational suppression and transcriptional remodeling with the appearance of protein aggregates, but whether these responses are induced by aggregates or their misfolded monomeric or oligomeric precursors remains unclear. Because aggregation in cells is rapid, nonlinear, and asynchronous, it has not been possible to deconvolve these kinetically linked processes to determine the earliest cellular responses to misfolded proteins. Upon removal of the synthetic, biologically inert ligand shield-1 (S1), AgDD, an engineered variant FK506-binding protein (FKBP1A), rapidly (t1 ⁄ 2 ϳ5 min) unfolds and self-associates, forming detergent-insoluble, microscopic cytoplasmic aggregates. Using global diglycine-capture (K-GG) proteomics, we found here that this solubility transition is associated with immediate increases in ubiquitylation of AgDD itself, along with that of endogenous proteins that are components of the ribosome and the 26S proteasome. We also found that the earliest cellular responses to acute S1 removal include recruitment of ubiquitin protein ligase E3C (UBE3C) to the 26S proteasome and ubiquitylation of two key proteasomal ubiquitin receptors, 26S proteasome regulatory subunit RPN10 (RPN10) and Rpn13 homolog (RPN13 or ADRM1). We conclude that these proteasomal responses are due to AgDD protein misfolding and not to the presence of detergent-insoluble aggregates.

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Protein misfolding specifies recruitment to cytoplasmic inclusion bodies

Abstract: Inclusion bodies containing aggregated disease-associated proteins and polyubiquitin conjugates are universal hallmarks of neurodegenerative diseases. Here, Bersuker et al. examine the necessity and sufficiency of ubiquitin conjugation for targeting proteins to inclusion bodies.

Cited by 35 publications

References 71 publications

Ubiquitin Accumulation on Disease Associated Protein Aggregates Is Correlated with Nuclear Ubiquitin Depletion, Histone De-Ubiquitination and Impaired DNA Damage Response

Ubiquitin Accumulation on Disease Associated Protein Aggregates Is Correlated with Nuclear Ubiquitin Depletion, Histone De-Ubiquitination and Impaired DNA Damage Response

Nascent-protein ubiquitination is required for heat shock–induced gene downregulation in human cells

Acute unfolding of a single protein immediately stimulates recruitment of ubiquitin protein ligase E3C (UBE3C) to 26S proteasomes

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