scholarly journals Compromising the 19S proteasome complex protects cells from reduced flux through the proteasome

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Peter Tsvetkov ◽  
Marc L Mendillo ◽  
Jinghui Zhao ◽  
Jan E Carette ◽  
Parker H Merrill ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Cellular Protein ◽  
Fitness Cost ◽  
Survival Advantage ◽  
Protein Homeostasis ◽  
Proteotoxic Stress ◽  
Genome Wide ◽  
Regulatory Complex ◽  
Modest Reduction ◽  
Specific Inhibitors

Proteasomes are central regulators of protein homeostasis in eukaryotes. Proteasome function is vulnerable to environmental insults, cellular protein imbalance and targeted pharmaceuticals. Yet, mechanisms that cells deploy to counteract inhibition of this central regulator are little understood. To find such mechanisms, we reduced flux through the proteasome to the point of toxicity with specific inhibitors and performed genome-wide screens for mutations that allowed cells to survive. Counter to expectation, reducing expression of individual subunits of the proteasome's 19S regulatory complex increased survival. Strong 19S reduction was cytotoxic but modest reduction protected cells from inhibitors. Protection was accompanied by an increased ratio of 20S to 26S proteasomes, preservation of protein degradation capacity and reduced proteotoxic stress. While compromise of 19S function can have a fitness cost under basal conditions, it provided a powerful survival advantage when proteasome function was impaired. This means of rebalancing proteostasis is conserved from yeast to humans.

scholarly journals Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kamran Rizzolo ◽  
Angela Yeou Hsiung Yu ◽  
Adedeji Ologbenla ◽  
Sa-Rang Kim ◽  
Haojie Zhu ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Protein Degradation ◽  
Degradation Rate ◽  
Cellular Protein ◽  
Trigger Factor ◽  
Protein Homeostasis ◽  
Functional Interaction ◽  
Functional Association ◽  
Gene Coding ◽  
Close Proximity

AbstractA functional association is uncovered between the ribosome-associated trigger factor (TF) chaperone and the ClpXP degradation complex. Bioinformatic analyses demonstrate conservation of the close proximity of tig, the gene coding for TF, and genes coding for ClpXP, suggesting a functional interaction. The effect of TF on ClpXP-dependent degradation varies based on the nature of substrate. While degradation of some substrates are slowed down or are unaffected by TF, surprisingly, TF increases the degradation rate of a third class of substrates. These include λ phage replication protein λO, master regulator of stationary phase RpoS, and SsrA-tagged proteins. Globally, TF acts to enhance the degradation of about 2% of newly synthesized proteins. TF is found to interact through multiple sites with ClpX in a highly dynamic fashion to promote protein degradation. This chaperone–protease cooperation constitutes a unique and likely ancestral aspect of cellular protein homeostasis in which TF acts as an adaptor for ClpXP.

scholarly journals Genome-wide analysis suggests the importance of vascular processes and neuroinflammation in late-life antidepressant response

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Victoria S. Marshe ◽  
Malgorzata Maciukiewicz ◽  
Anne-Christin Hauschild ◽  
Farhana Islam ◽  
Li Qin ◽  
...  
Keyword(s):  
Older Adults ◽  
Cerebrovascular Disease ◽  
Protein Degradation ◽  
Late Life ◽  
Cardioembolic Stroke ◽  
Symptom Improvement ◽  
Antidepressant Response ◽  
Polygenic Risk ◽  
Remission Status ◽  
Genome Wide

AbstractAntidepressant outcomes in older adults with depression is poor, possibly because of comorbidities such as cerebrovascular disease. Therefore, we leveraged multiple genome-wide approaches to understand the genetic architecture of antidepressant response. Our sample included 307 older adults (≥60 years) with current major depression, treated with venlafaxine extended-release for 12 weeks. A standard genome-wide association study (GWAS) was conducted for post-treatment remission status, followed by in silico biological characterization of associated genes, as well as polygenic risk scoring for depression, neurodegenerative and cerebrovascular disease. The top-associated variants for remission status and percentage symptom improvement were PIEZO1 rs12597726 (OR = 0.33 [0.21, 0.51], p = 1.42 × 10−6) and intergenic rs6916777 (Beta = 14.03 [8.47, 19.59], p = 1.25 × 10−6), respectively. Pathway analysis revealed significant contributions from genes involved in the ubiquitin-proteasome system, which regulates intracellular protein degradation with has implications for inflammation, as well as atherosclerotic cardiovascular disease (n = 25 of 190 genes, p = 8.03 × 10−6, FDR-corrected p = 0.01). Given the polygenicity of complex outcomes such as antidepressant response, we also explored 11 polygenic risk scores associated with risk for Alzheimer’s disease and stroke. Of the 11 scores, risk for cardioembolic stroke was the second-best predictor of non-remission, after being male (Accuracy = 0.70 [0.59, 0.79], Sensitivity = 0.72, Specificity = 0.67; p = 2.45 × 10−4). Although our findings did not reach genome-wide significance, they point to previously-implicated mechanisms and provide support for the roles of vascular and inflammatory pathways in LLD. Overall, significant enrichment of genes involved in protein degradation pathways that may be impaired, as well as the predictive capacity of risk for cardioembolic stroke, support a link between late-life depression remission and risk for vascular dysfunction.

scholarly journals Substrate-Specific Effects of Natural Genetic Variation on Proteasome Activity

2021 ◽  
Author(s):  
Mahlon Collins ◽  
Randi R. Avery ◽  
Frank W Albert
Keyword(s):  
Genetic Variation ◽  
Protein Degradation ◽  
Dynamic Control ◽  
Cellular Protein ◽  
Proteasome Activity ◽  
Heritable Variation ◽  
Natural Genetic Variation ◽  
Specific Effects ◽  
Regulatory Particle

The bulk of targeted cellular protein degradation is performed by the proteasome, a multi-subunit complex consisting of the 19S regulatory particle, which binds, unfolds, and translocates substrate proteins, and the 20S core particle, which degrades them. Protein homeostasis requires precise, dynamic control of proteasome activity. To what extent genetic variation creates differences in proteasome activity is almost entirely unknown. Using the ubiquitin-independent degrons of the ornithine decarboxylase and Rpn4 proteins, we developed reporters that provide high-throughput, quantitative measurements of proteasome activity in vivo in genetically diverse cell populations. We used these reporters to characterize the genetic basis of variation in proteasome activity in the yeast Saccharomyces cerevisiae. We found that proteasome activity is a complex, polygenic trait, shaped by variation throughout the genome. Genetic influences on proteasome activity were predominantly substrate-specific, suggesting that they primarily affect the function or activity of the 19S regulatory particle. Our results demonstrate that individual genetic differences create heritable variation in proteasome activity and suggest that genetic effects on proteasomal protein degradation may be an important source of variation in cellular and organismal traits.

scholarly journals Biosynthesis of Coenzyme Q in the Phytopathogen Xanthomonas campestris via a Yeast-Like Pathway

2019 ◽  
Vol 32 (2) ◽  
pp. 217-226 ◽  
Author(s):  
Lian Zhou ◽  
Ming Li ◽  
Xing-Yu Wang ◽  
Hao Liu ◽  
Shuang Sun ◽  
...  
Keyword(s):  
Xanthomonas Campestris ◽  
Coenzyme Q ◽  
Regulatory Mechanisms ◽  
Membrane Component ◽  
E Coli ◽  
Regulatory Complex ◽  
Iron Carboxylate ◽  
Xanthomonas Campestris Pv Campestris ◽  
Specific Inhibitors ◽  
Novel Protein

Coenzyme Q (CoQ) is a lipid-soluble membrane component found in organisms ranging from bacteria to mammals. The biosynthesis of CoQ has been intensively studied in Escherichia coli, where 12 genes (ubiA, -B, -C, -D, -E, -F, -G, -H, -I, -J, -K, and -X) are involved. In this study, we first investigated the putative genes for CoQ8 biosynthesis in the phytopathogen Xanthomonas campestris pv. campestris using a combination of bioinformatic, genetic, and biochemical methods. We showed that Xc_0489 (coq7Xc) encodes a di-iron carboxylate monooxygenase filling the E. coli UbiF role for hydroxylation at C-6 of the aromatic ring. Xc_0233 (ubiJXc) encodes a novel protein with an E. coli UbiJ-like domain organization and is required for CoQ8 biosynthesis. The X. campestris pv. campestris decarboxylase gene remains unidentified. Further functional analysis showed that ubiB and ubiK homologs ubiBXc and ubiKXc are required for CoQ8 biosynthesis in X. campestris pv. campestris. Deletion of ubiJXc, ubiBXc, and ubiKXc led to the accumulation of an intermediate 3-octaprenyl-4-hydroxybenzoic acid. UbiKXc interacts with UbiJXc and UbiBXc to form a regulatory complex. Deletion analyses of these CoQ8 biosynthetic genes indicated that they are important for virulence in Chinese radish. These results suggest that the X. campestris pv. campestris CoQ8 biosynthetic reactions and regulatory mechanisms are divergent from those of E. coli. The variations provide an opportunity for the design of highly specific inhibitors for the prevention of infection by the phytopathogen X. campestris pv. campestris.

scholarly journals ER stress causes widespread protein aggregation and prion formation

2017 ◽  
Vol 216 (8) ◽  
pp. 2295-2304 ◽  
Author(s):  
Norfadilah Hamdan ◽  
Paraskevi Kritsiligkou ◽  
Chris M. Grant
Keyword(s):  
Protein Aggregation ◽  
Er Stress ◽  
Secretory Pathway ◽  
Cellular Protein ◽  
Protein Homeostasis ◽  
Er Quality Control ◽  
Unfolded Protein ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Er Homeostasis

Disturbances in endoplasmic reticulum (ER) homeostasis create a condition termed ER stress. This activates the unfolded protein response (UPR), which alters the expression of many genes involved in ER quality control. We show here that ER stress causes the aggregation of proteins, most of which are not ER or secretory pathway proteins. Proteomic analysis of the aggregated proteins revealed enrichment for intrinsically aggregation-prone proteins rather than proteins which are affected in a stress-specific manner. Aggregation does not arise because of overwhelming proteasome-mediated degradation but because of a general disruption of cellular protein homeostasis. We further show that overexpression of certain chaperones abrogates protein aggregation and protects a UPR mutant against ER stress conditions. The onset of ER stress is known to correlate with various disease processes, and our data indicate that widespread amorphous and amyloid protein aggregation is an unanticipated outcome of such stress.

scholarly journals Chaperones and Proteostasis: Role in Parkinson’s Disease

Diseases ◽  
2020 ◽  
Vol 8 (2) ◽  
pp. 24 ◽  
Author(s):  
Neha Joshi ◽  
Atchaya Raveendran ◽  
Shirisha Nagotu
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Three Dimensional ◽  
Cellular Protein ◽  
The Body ◽  
Dimensional Structure ◽  
Protein Homeostasis ◽  
Altered Expression ◽  
And Function ◽  
Related Proteins

Proper folding to attain a defined three-dimensional structure is a prerequisite for the functionality of a protein. Improper folding that eventually leads to formation of protein aggregates is a hallmark of several neurodegenerative disorders. Loss of protein homeostasis triggered by cellular stress conditions is a major contributing factor for the formation of these toxic aggregates. A conserved class of proteins called chaperones and co-chaperones is implicated in maintaining the cellular protein homeostasis. Expanding the body of evidence highlights the role of chaperones as central mediators in the formation, de-aggregation and degradation of the aggregates. Altered expression and function of chaperones is associated with many neurodegenerative diseases including Parkinson’s disease. Several studies indicate that chaperones are at the center of the cause and effect cycle of this disease. An overview of the various chaperones that are associated with homeostasis of Parkinson’s disease-related proteins and their role in pathogenicity will be discussed in this review.

scholarly journals Locked in a vicious cycle: the connection between genomic instability and a loss of protein homeostasis

2020 ◽  
Author(s):  
Wouter Huiting ◽  
Steven Bergink
Keyword(s):  
Control Systems ◽  
Genomic Instability ◽  
Therapeutic Strategy ◽  
Protein Quality ◽  
Accelerated Ageing ◽  
Protein Homeostasis ◽  
Vicious Cycle ◽  
Proteotoxic Stress ◽  
Gradual Loss ◽  
Wide Range

AbstractCardiomyopathies, neuropathies, cancer and accelerated ageing are unequivocally distinct diseases, yet they also show overlapping pathological hallmarks, including a gradual loss of genomic integrity and proteotoxic stress. Recent lines of evidence suggest that this overlap could be the result of remarkably interconnected molecular cascades between nuclear genomic instability and a loss of protein homeostasis. In this review, we discuss these complex connections, as well as their possible impact on disease. We focus in particular on the inherent ability of a wide range of genomic alterations to challenge protein homeostasis. In doing so, we provide evidence suggesting that a loss of protein homeostasis could be a far more prevalent consequence of genomic instability than generally believed. In certain cases, such as aneuploidy, a loss of protein homeostasis appears to be a crucial mechanism for pathology, which indicates that enhancing protein quality control systems could be a promising therapeutic strategy in diseases associated with genomic instability.

scholarly journals Insulin and Analogue Effects on Protein Degradation in Different Cell Types

2000 ◽  
Vol 276 (15) ◽  
pp. 11552-11558 ◽  
Author(s):  
Janet Fawcett ◽  
Frederick G. Hamel ◽  
Robert G. Bennett ◽  
Zoltan Vajo ◽  
William C. Duckworth
Keyword(s):  
Protein Degradation ◽  
Hepg2 Cells ◽  
Cell Types ◽  
Major Effect ◽  
Cellular Protein ◽  
Experimental Conditions ◽  
L6 Cells ◽  
Different Cell Types

In adult animals, the major effect of insulin on protein turnover is inhibition of protein degradation. Cellular protein degradation is under the control of multiple systems, including lysosomes, proteasomes, calpains, and giant protease. Insulin has been shown to alter proteasome activityin vitroandin vivo. We examined the inhibition of protein degradation by insulin and insulin analogues (LysB28,ProB29-insulin (LysPro), AspB10-insulin (B10), and GluB4,GlnB16,PheB17-insulin (EQF)) in H4, HepG2, and L6 cells. These effects were compared with receptor binding. Protein degradation was examined by release of trichloroacetic acid-soluble radioactivity from cells previously labeled with [3H]leucine. Short- and intermediate-lived proteins were examined. H4 cells bound insulin with an EC50of 4.6 × 10−9m. LysPro was similar. The affinity of B10 was increased 2-fold; that of EQF decreased 15-fold. Protein degradation inhibition in H4 cells was highly sensitive to insulin (EC50= 4.2 × 10−11and 1.6 × 10−10m, short- and intermediate-lived protein degradation, respectively) and analogues. Despite similar binding, LysPro was 11- to 18-fold more potent than insulin at inhibiting protein degradation. Conversely, although EQF showed lower binding to H4 cells than insulin, its action was similar. The relative binding potencies of analogues in HepG2 cells were similar to those in H4 cells. Examination of protein degradation showed insulin, LysPro, and B10 were equivalent while EQF was less potent. L6 cells showed no difference in the binding of the analogues compared with insulin, but their effect on protein degradation was similar to that seen in HepG2 cells except B10 inhibited intermediate-lived protein degradation better than insulin. These studies illustrate the complexities of cellular protein degradation and the effects of insulin. The effect of insulin and analogues on protein degradation vary significantly in different cell types and with different experimental conditions. The differences seen in the action of the analogues cannot be attributed to binding differences. Post-receptor mechanisms, including intracellular processing and degradation, must be considered.

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