scholarly journals A general in vitro assay to study enzymatic activities of the ubiquitin system

2019 ◽  
Author(s):  
Yukun Zuo ◽  
Boon Keat Chong ◽  
Kun Jiang ◽  
Daniel Finley ◽  
David Klenerman ◽  
...  

AbstractThe ubiquitin (Ub) system regulates a wide range of cellular signaling pathways. Several hundred E1, E2 and E3 enzymes are together responsible for protein ubiquitination, thereby controlling cellular activities. Due to the numerous enzymes and processes involved, studies on ubiquitination activities have been challenging. We here report a novel FRET-based assay to study the in vitro kinetics of ubiquitination. FRET is established between binding of fluorophore-labeled Ub to eGFP-tagged ZnUBP, a domain that exclusively binds unconjugated Ub. We name this assay the Free Ub Sensor System (FUSS). Using Uba1, UbcH5 and CHIP as model E1, E2 and E3 enzymes, respectively, we demonstrate that ubiquitination results in decreasing FRET efficiency, from which reaction rates can be determined. Further treatment with USP21, a deubiquitinase, leads to increased FRET efficiency, confirming the reversibility of the assay. We subsequently use this assay to show that increasing the concentration of CHIP or UbcH5 but not Uba1 enhances ubiquitination rates, and develop a novel machine learning approach to model ubiquitination. The overall ubiquitination activity is also increased upon incubation with tau, a substrate of CHIP. Our data together demonstrate the versatile applications of a novel ubiquitination assay that does not require labeling of E1, E2, E3 or substrates, and is thus likely compatible with any E1-E2-E3 combinations.

2004 ◽  
Vol 186 (16) ◽  
pp. 5392-5399 ◽  
Author(s):  
Frank J. Grundy ◽  
Tina M. Henkin

ABSTRACT Binding of uncharged tRNA to the nascent transcript promotes readthrough of a leader region transcription termination signal in genes regulated by the T box transcription antitermination mechanism. Each gene in the T box family responds independently to its cognate tRNA, with specificity determined by base pairing of the tRNA to the leader at the anticodon and acceptor ends of the tRNA. tRNA binding stabilizes an antiterminator element in the transcript that sequesters sequences that participate in formation of the terminator helix. tRNAGly-dependent antitermination of the Bacillus subtilis glyQS leader was previously demonstrated in a purified in vitro assay system. This assay system was used to investigate the kinetics of transcription through the glyQS leader and the effect of tRNA and transcription elongation factors NusA and NusG on transcriptional pausing and antitermination. Several pause sites, including a major site in the loop of stem III of the leader, were identified, and the effect of modulation of pausing on antitermination efficiency was analyzed. We found that addition of tRNAGly can promote antitermination as long as the tRNA is added before the majority of the transcription complexes reach the termination site, and variations in pausing affect the requirements for timing of tRNA addition.


Biochemistry ◽  
2020 ◽  
Vol 59 (7) ◽  
pp. 851-861 ◽  
Author(s):  
Yukun Zuo ◽  
Boon Keat Chong ◽  
Kun Jiang ◽  
Daniel Finley ◽  
David Klenerman ◽  
...  

2011 ◽  
Vol 156 (3) ◽  
pp. 307-314 ◽  
Author(s):  
B.J. Crielaard ◽  
A. Yousefi ◽  
J.P. Schillemans ◽  
C. Vermehren ◽  
K. Buyens ◽  
...  

2018 ◽  
Vol 12 (1) ◽  
pp. 14-23 ◽  
Author(s):  
Anand Mohan Verma ◽  
Nanda Kishore

Object: Excessive amount of oxygen content in unprocessed bio-oil deteriorates the quality of bio-oil which cannot be used in transportation vehicles without upgrading. Acetic acid (CH3COOH) is a vital component of ‘acids’ catalogue of unprocessed bio-oil produced from thermochemical conversions of most of biomass feedstocks such as switchgrass, alfalfa, etc. In this study, the decomposition reactions of acetic acid are carried out by two reaction pathways, i.e., decarboxylation and dehydration reactions. In addition, the reaction rates of decomposition are analysed in a wide range of temperatures, i.e., 298-900 K and at atmospheric pressure. Method: All quantum chemical calculations are performed in the gas phase using two DFT functionals, B3LYP and M06-2X, with 6-31g(d) basis set. The dehydration reaction of acetic acid proceeds directly from ground state structure of acetic acid, whereas, decarboxylation reaction forms an unstable intermediate of acetic acid to initiate the proton migration. Barrier height and kinetics study for both reactions and theories are different and illustrated in the reaction pathway and rate profiles, respectively. Furthermore, both levels of theories offer similar structural configurations but they differ slightly in energetics. Conclusion: The reaction kinetics of both reactions is linearly fitted and the Arrhenius equations corresponding to each decomposition mechanism are generated by fitting the data from line equation.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 192-192
Author(s):  
Yuki Fujioka ◽  
Hiroyoshi Nishikawa ◽  
Naoto Takahashi

Introduction: Imatinib, the first tyrosine kinase inhibitor (TKI), has dramatically improved the prognosis of chronic myeloid leukemia (CML) patients. Recently, many trials of TKI discontinuation revealed that approximately 40% to 60% of CML patients who treated long time TKI therapy reached the treatment free remission (TFR), thus now TFR is proposed as one of the goals in CML treatment. Achieving deep molecular response (DMR) by TKI therapy is a minimum requirement of challenge to TKI discontinuation in CML patient, actually CML patients with molecular residual disease (MRD) showed worse consequence than undetectable MRD (IJH 2017). On the other hand, it was known that some patients have continued TFR with detectable BCR-ABL fusion gene, these patients hadn't shown indubitable molecular relapse while BCR-ABL+ malignant cells continued to exist for prolonged time. We hypothesized that the malignant cells were eliminated by host immune systems in these fluctuated patients. Here, we focused on T-cell response, so we analyzed T-cell related markers to identify biomarkers that can predict patients which can continue TFR or not in Japanese CML patients. Furthermore, we confirmed the action of imatinib for T-cell response in vitro. Methods: Japanese CML patients treated with imatinib for at least three years and confirmed in DMR for at least two years were eligible. Patients who received other TKI or stem cell transplantations were excluded. Patients were re-confirmed in MR4.5 before discontinue imatinib and they were sampled peripheral blood at pre- and 1, 3 months after stopping imatinib (figure 1). Peripheral blood mononuclear cells (PBMCs) were subjected to staining with T-cell markers and analyzed by mass cytometry and flowcytometry. Plasma were subjected to detecting Imatinib trough concentrations. Purchased PBMCs of healthy individuals were cultured and analyzed by flowcytometry in vitro assay. Results: Samples of 68 CML patients were analyzed. We classified these CML patients into two groups (Non-retreatment and Retreatment groups) by clinical courses after stopping imatinib (figure 2). Frequency of CD4+ T cells and CD8+ T cells in CD3+ T cells were no difference between both groups. FoxP3+CD4+ regulatory T cells (Treg) were also no difference between both groups, but kinetics of Treg, especially Fraction II (Fr.II : FoxP3hiCD45RA-) of Treg from Pre-stopping imatinib to 1 month after stopping imatinib significantly increased in non-retreatment groups. Kinetics of Treg / CD8+ T cells ratio also significantly increased in non-retreatment groups, and predicted curve made by these kinetics of each groups were significant (figure 3). The expression of PD-1 or other suppressive co-stimulatory molecules in CD8+ T cells of non-retreatment groups at after stopping imatinib had tendency to decrease. Phosphorylated LCK in CD8+ T cells of non-retreatment groups at after stopping imatinib had tendency to increase. Next, we did in vitro assay to confirm the effect of pre-treatment of imatinib in imatinib free T cells. Pre-treatment of imatinib suppressed the proliferations of Treg Fr.II after TCR stimulation dose dependently, but not CD8+ T cells (figure 4). Frequency of phosphorylated LCK in Treg Fr.II increased after TCR stimulation even if pre-treated imatinib at reasonable dose, but didn't increased under the condition of high dose imatinib. Conclusion: Treg population and Treg / CD8+ T cells ratio in PBMCs elevated after stopping imatinib in non-retreatment groups of CML patients. Population of CD8+ T cells showed no differences in two groups but CD8+ T cells were tending to activate after stopping imatinib in non-retreatment groups. These data indicate that the kinetics of Treg after stopping imatinib connect with the immune response of imatinib discontinued CML patients. In vitro data indicate that Treg were more sensitive for imatinib treatment than CD8+ T cells, so kinetics of Treg may possibly become the biomarker of ability of immune responses. Our data suggested that optimum imatinib exposure induce appropriate immune responses leading good prognosis, and excess imatinib exposure induce exhaust immune responses leading poor prognosis. Disclosures Nishikawa: Taihou Pharmaceuticals: Research Funding; Kyowa Hakko Kirin: Research Funding; Bristol-Myers Squibb: Research Funding, Speakers Bureau; Ono Pharmaceutical: Research Funding, Speakers Bureau; Chugai Pharmaceuticals: Research Funding, Speakers Bureau; Asahikasei Pharma: Research Funding; Sysmex: Research Funding; Daiichi Sankyo: Research Funding; Zennyaku: Research Funding. Takahashi:Otsuka Pharmaceutical: Research Funding, Speakers Bureau; Novartis Pharmaceuticals: Research Funding, Speakers Bureau; Chug Pharmaceuticals: Research Funding; Pfizer: Research Funding, Speakers Bureau; Asahi Kasei Pharma: Research Funding; Bristol-Myers Squibb: Speakers Bureau; Kyowa Hakko Kirin: Research Funding; Eisai Pharmaceuticals: Research Funding; Astellas Pharma: Research Funding; Ono Pharmaceutical: Research Funding.


2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Min Zhang ◽  
Wei Liu ◽  
Qingan Zhang ◽  
Hongfeng Hu

Parkinson’s disease (PD) is a neurodegenerative disorder characterized by progressive neuronal loss in different brain regions, including the dopaminergic (DA) neurons of the substantia nigra pars compacta (SNc). The aggregation of α-synuclein (α-Syn) plays an essential role in the progression of PD-related neuron toxicity. In this study, bioinformatic analysis was used to confirm differentially expressed genes between patients with PD and healthy donors. Immunofluorescence was used to study the aggregation of α-Syn. Flow cytometry was used to confirm the apoptosis of neurons. Western blot was used to investigate the underlying mechanism. Coimmunoprecipitation (co-IP) was used to verify the interaction between proteins. Luciferase activity assay was used to confirm the target gene of miRNA. In vitro protein ubiquitination assay was used to ascertain the role of S-phase kinase-associated protein 1 (SKP1) on the ubiquitination processes of polo-like kinase 2 (PLK2). The result indicated that miR-101-3p was overexpressed in the substantia nigra of the postmortem brains of patients with PD. The underlying role was investigated in the SH-SY5Y cell line. The overexpression of α-Syn did not result in toxicity or aggregation. However, the co-overexpression of miR-101-3p and α-Syn promoted aggregation and neuron toxicity. Luciferase activity assay indicated that SKP1 is a target gene of miR-101-3p. The co-IP experiment confirmed that SKP1 could directly interact with PLK2. In vitro protein ubiquitination assay confirmed that SKP1 could promote the ubiquitination and subsequent protein degradation of PLK2. We also observed that the cotransfection of short hairpin RNA that targets PLK2 and α-Syn overexpression plasmid results in the endoplasmic reticulum stress of neurons. Our results collectively provide evidence that miR-101-3p contributes to α-Syn aggregation in neurons through the miR-101-3p/SKP1/PLK2 pathway.


2004 ◽  
Vol 32 (6) ◽  
pp. 1057-1059 ◽  
Author(s):  
A.D. Postle ◽  
H. Dombrowsky ◽  
H. Clarke ◽  
C.J. Pynn ◽  
G. Koster ◽  
...  

Mammalian cell PtdIns (phosphatidylinositol) in vivo is enriched in the sn-1-stearoyl 2-arachidonoyl species, the physiological precursor of phosphatidylinositol 4,5-bisphosphate. Mechanisms regulating this specificity are unclear but are typically lost for cells in culture. We used ESI-MS (tandem electrospray ionization-mass spectrometry) to determine the molecular species of PtdIns synthesized by mouse tissues in vivo compared with cultured cells in vitro. After incorporation of deuteriated myo-d6-inositol over 3 h, endogenous and newly synthesized PtdIns and lysoPtdIns species were quantified from precursor scans of m/z 241− and m/z 247− respectively. PtdIns was synthesized as a wide range of species irrespective of the final membrane composition. Analyses of isotope enrichments argued against acyl remodelling as the major regulatory mechanism: composition of the lysoPtdIns pool under all conditions reflected that of either endogenous or newly synthesized PtdIns and was always at equilibrium. The kinetics of PtdIns synthesis, together with the prolonged time scale required for achieving final equilibrium compositions suggest that selective transport between membranes and/or hydrolysis of selected molecular species are the most probable mechanisms regulating compositions of PtdIns and, ultimately, phosphatidylinositol 4,5-bisphosphate.


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