The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features

N6-methyladenosine (m(6)A) and N6,2 '-O-dimethyladenosine (m(6)Am) are two abundant modifications found in mRNAs and ncRNAs that can regulate multiple aspects of RNA biology. They function mainly by regulating interactions with specific RNA-binding proteins. Both modifications are linked to development, disease and stress response. To date, three methyltransferases and two demethylases have been identified that modify adenosines in mammalian mRNAs. Here, we present a comprehensive analysis of the interactomes of these enzymes. PCIF1 protein network comprises mostly factors involved in nascent RNA synthesis by RNA polymerase II, whereas ALKBH5 is closely linked with most aspects of pre-mRNA processing and mRNA export to the cytoplasm. METTL16 resides in subcellular compartments co-inhabited by several other RNA modifiers and processing factors. FTO interactome positions this demethylase at a crossroad between RNA transcription, RNA processing and DNA replication and repair. Altogether, these enzymes share limited spatial interactomes, pointing to specific molecular mechanisms of their regulation.Peer reviewe

Elimination Voltammetry with Linear Scan as a New Detection Method for DNA Sensors

The paper describes successful coupling of adsorptive transfer stripping (AdTS) andelimination voltammetry with linear scan (EVLS) for the resolution of reduction signals of cytosine (C)and adenine (A) residues in hetero-oligodeoxynucleotides (ODNs). Short ODNs (9-mers and 20-mers)were adsorbed from a small volume on a hanging mercury drop electrode (HMDE). After washing ofthe ODN-modified electrode by water and its transferring to an electrochemical cell, voltammetric curves were measured. The AdTS EVLS was able to determine of C/A ratio of ODNs through theelimination function conserving the diffusion current component and eliminating kinetic and chargingcurrent components. This function, which provides the elimination signal in a peak-counterpeak form,increased the current sensitivity for A and C resolution, and for the recognition of bases sequences inODN chains. Optimal conditions of elimination experiments such as pH, time of adsorption, and scanrate were found. The combination of EVLS with AdTS procedure can be considered as a newdetection method in a DNA sensor

Role of Nse1 Subunit of SMC5/6 Complex as a Ubiquitin Ligase

Structural Maintenance of Chromosomes (SMC) complexes are important for many aspects of the chromosomal organization. Unlike cohesin and condensin, the SMC5/6 complex contains a variant RING domain carried by its Nse1 subunit. RING domains are characteristic for ubiquitin ligases, and human NSE1 has been shown to possess ubiquitin-ligase activity in vitro. However, other studies were unable to show such activity. Here, we confirm Nse1 ubiquitin-ligase activity using purified Schizosaccharomyces pombe proteins. We demonstrate that the Nse1 ligase activity is stimulated by Nse3 and Nse4. We show that Nse1 specifically utilizes Ubc13/Mms2 E2 enzyme and interacts directly with ubiquitin. We identify the Nse1 mutation (R188E) that specifically disrupts its E3 activity and demonstrate that the Nse1-dependent ubiquitination is particularly important under replication stress. Moreover, we determine Nse4 (lysine K181) as the first known SMC5/6-associated Nse1 substrate. Interestingly, abolition of Nse4 modification at K181 leads to suppression of DNA-damage sensitivity of other SMC5/6 mutants. Altogether, this study brings new evidence for Nse1 ubiquitin ligase activity, significantly advancing our understanding of this enigmatic SMC5/6 function

Transgelin Contributes to a Poor Response of Metastatic Renal Cell Carcinoma to Sunitinib Treatment

Renal cell carcinoma (RCC) represents about 2–3% of all cancers with over 400,000 new cases per year. Sunitinib, a vascular endothelial growth factor tyrosine kinase receptor inhibitor, has been used mainly for first-line treatment of metastatic clear-cell RCC with good or intermediate prognosis. However, about one-third of metastatic RCC patients do not respond to sunitinib, leading to disease progression. Here, we aim to find and characterize proteins associated with poor sunitinib response in a pilot proteomics study. Sixteen RCC tumors from patients responding (8) vs. non-responding (8) to sunitinib 3 months after treatment initiation were analyzed using data-independent acquisition mass spectrometry, together with their adjacent non-cancerous tissues. Proteomics analysis quantified 1996 protein groups (FDR = 0.01) and revealed 27 proteins deregulated between tumors non-responding vs. responding to sunitinib, representing a pattern of deregulated proteins potentially contributing to sunitinib resistance. Gene set enrichment analysis showed an up-regulation of epithelial-to-mesenchymal transition with transgelin as one of the most significantly abundant proteins. Transgelin expression was silenced by CRISPR/Cas9 and RNA interference, and the cells with reduced transgelin level exhibited significantly slower proliferation. Our data indicate that transgelin is an essential protein supporting RCC cell proliferation, which could contribute to intrinsic sunitinib resistance

Desmocollin-1 is associated with pro-metastatic phenotype of luminal A breast cancer cells and is modulated by parthenolide

Abstract Background Desmocollin-1 (DSC1) is a desmosomal transmembrane glycoprotein that maintains cell-to-cell adhesion. DSC1 was previously associated with lymph node metastasis of luminal A breast tumors and was found to increase migration and invasion of MCF7 cells in vitro. Therefore, we focused on DSC1 role in cellular and molecular mechanisms in luminal A breast cancer and its possible therapeutic modulation. Methods Western blotting was used to select potential inhibitor decreasing DSC1 protein level in MCF7 cell line. Using atomic force microscopy we evaluated effect of DSC1 overexpression and modulation on cell morphology. The LC–MS/MS analysis of total proteome on Orbitrap Lumos and RNA-Seq analysis of total transcriptome on Illumina NextSeq 500 were performed to study the molecular mechanisms associated with DSC1. Pull-down analysis with LC–MS/MS detection was carried out to uncover DSC1 protein interactome in MCF7 cells. Results Analysis of DSC1 protein levels in response to selected inhibitors displays significant DSC1 downregulation (p-value ≤ 0.01) in MCF7 cells treated with NF-κB inhibitor parthenolide. Analysis of mechanic cell properties in response to DSC1 overexpression and parthenolide treatment using atomic force microscopy reveals that DSC1 overexpression reduces height of MCF7 cells and conversely, parthenolide decreases cell stiffness of MCF7 cells overexpressing DSC1. The LC–MS/MS total proteome analysis in data-independent acquisition mode shows a strong connection between DSC1 overexpression and increased levels of proteins LACRT and IGFBP5, increased expression of IGFBP5 is confirmed by RNA-Seq. Pathway analysis of proteomics data uncovers enrichment of proliferative MCM_BIOCARTA pathway including CDK2 and MCM2-7 after DSC1 overexpression. Parthenolide decreases expression of LACRT, IGFBP5 and MCM_BIOCARTA pathway specifically in DSC1 overexpressing cells. Pull-down assay identifies DSC1 interactions with cadherin family proteins including DSG2, CDH1, CDH3 and tyrosine kinase receptors HER2 and HER3; parthenolide modulates DSC1-HER3 interaction. Conclusions Our systems biology data indicate that DSC1 is connected to mechanisms of cell cycle regulation in luminal A breast cancer cells, and can be effectively modulated by parthenolide. Graphical Abstrac

Phytochelatin Modified Electrode Surface as a Sensitive Heavy- Metal Ion Biosensor

Electrochemical biosensors have superior properties over other existingmeasurement systems because they can provide rapid, simple and low-cost on-fielddetermination of many biological active species and a number of dangerous pollutants. Inour work, we suggested a new heavy metal biosensor based on interaction of heavy metalions (Cd2+ and Zn2+ ) with phytochelatin, which was adsorbed on the surface of the hangingmercury drop electrode, using adsorptive transfer stripping differential pulse voltammetry.In addition, we applied the suggested technique for the determination of heavy metals in abiological sample – human urine and platinum in a pharmaceutical drug. The detectionlimits (3 S/N) of Cd(II), Zn(II) and cis-platin were about 1.0, 13.3 and 1.9 pmole in 5 μl,respectively. On the basis of the obtained results, we propose that the suggested techniqueoffers simple, rapid, and low-cost detection of heavy metals in environmental, biologicaland medical samples

Phytochelatin modified electrode surface as a sensitive heavy-metal ion biosensor. Sensors 2005

Abstract: Electrochemical biosensors have superior properties over other existing measurement systems because they can provide rapid, simple and low-cost on-field determination of many biological active species and a number of dangerous pollutants. In our work, we suggested a new heavy metal biosensor based on interaction of heavy metal ions (Cd 2+ and Zn 2+) with phytochelatin, which was adsorbed on the surface of the hanging mercury drop electrode, using adsorptive transfer stripping differential pulse voltammetry. In addition, we applied the suggested technique for the determination of heavy metals in a biological sample – human urine and platinum in a pharmaceutical drug. The detection limits (3 S/N) of Cd(II), Zn(II) and cis-platin were about 1.0, 13.3 and 1.9 pmole in 5 µl, respectively. On the basis of the obtained results, we propose that the suggested technique offers simple, rapid, and low-cost detection of heavy metals in environmental, biological and medical samples

Electrochemical Sensors for Detection of Acetylsalicylic Acid

Acetylsalicylic acid (AcSA), or aspirin, was introduced in the late 1890s and hasbeen used to treat a variety of inflammatory conditions. The aim of this work was to suggestelectrochemical sensor for acetylsalicylic detection. Primarily, we utilized square wavevoltammetry (SWV) using both carbon paste electrode (CPE) and of graphite pencilelectrode (GPE) as working ones to indirect determination of AcSA. The principle ofindirect determination of AcSA bases in its hydrolysis on salicylic acid (SA), which isconsequently detected. Thus, we optimized both determination of SA and conditions forAcSA hydrolysis and found out that the most suitable frequency, amplitude, step potentialand the composition and pH of the supporting electrolyte for the determination of SA was260 Hz, 50 mV, 10 mV and Britton-Robinson buffer (pH 1.81), respectively. The detectionlimit (S/N = 3) of the SA was 1.3 ng/ml. After that, we aimed on indirect determination ofAcSA by SWV CPE. We tested the influence of pH of Britton-Robinson buffer andtemperature on yield of hydrolysis, and found out that 100% hydrolysis of AcSA wasreached after 80 minutes at pH 1.81 and 90°C. The method for indirect determination ofAcSA has been utilized to analyse pharmaceutical drug. The determined amount of AcSA in the pharmaceutical drug was in good agreement with the declared amounts. Moreover, weused GPE for determination of AcSA in a pharmaceutical drug. Base of the results obtainedfrom stationary electrochemical instrument we used flow injection analysis withelectrochemical detection to determine of salicylates (SA, AcSA, thiosalicylic acid, 3,5-dinitrosalicylic acid and 5-sulfosalicylic acid – SuSA). We found out that we are able todetermine all of detected salicylates directly without any pre-treatment, hydrolysis and so onat units of femtomoles per injection (5 μl)