Large-scale Purification of Type III Toxin-antitoxin Ribonucleoprotein Complex and its Components from Escherichia coli for Biophysical Studies

Toxin-antitoxin (TA) systems are widespread bacterial immune systems that confer protection against various environmental stresses. TA systems have been classified into eight types (I-VIII) based on the nature and mechanism of action of the antitoxin. Type III TA systems consist of a noncoding RNA antitoxin and a protein toxin, forming a ribonucleoprotein (RNP) TA complex that plays crucial roles in phage defence in bacteria. Type III TA systems are present in the human gut microbiome and several pathogenic bacteria and, therefore, could be exploited for a novel antibacterial strategy. Due to the inherent toxicity of the toxin for E. coli, it is challenging to overexpress and purify free toxins from E. coli expression systems. Therefore, protein toxin is typically co-expressed and co-purified with antitoxin RNA as an RNP complex from E. coli for structural and biophysical studies. Here, we have optimized the co-expression and purification method for ToxIN type III TA complexes from E. coli that results in the purification of TA RNP complex and, often, free antitoxin RNA and free active toxin in quantities required for the biophysical and structural studies. This protocol can also be adapted to purify isotopically labelled (e.g., uniformly 15N- or 13C-labelled) free toxin proteins, free antitoxin RNAs, and TA RNPs, which can be studied using multidimensional nuclear magnetic resonance (NMR) spectroscopy methods. Key features Detailed protocol for the large-scale purification of ToxIN type III toxin-antitoxin complexes from E. coli. The optimized protocol results in obtaining milligrams of TA RNP complex, free toxin, and free antitoxin RNA. Commercially available plasmid vectors and chemicals are used to complete the protocol in five days after obtaining the required DNA clones. The purified TA complex, toxin protein, and antitoxin RNA are used for biophysical experiments such as NMR, ITC, and X-ray crystallography.

Digital PCR-based evaluation of nucleic acid extraction kit performance for the co-purification of cell-free DNA and RNA

BACKGROUND

Blood plasma, one of the most studied liquid biopsies, contains various molecules that have biomarker potential for cancer detection, including cell-free DNA (cfDNA) and cell-free RNA (cfRNA). As the vast majority of cell-free nucleic acids in circulation are non-cancerous, a laboratory workflow with a high detection sensitivity of tumor-derived nucleic acids is a prerequisite for precision oncology. One way to meet this requirement is by the combined analysis of cfDNA and cfRNA from the same liquid biopsy sample. So far, no study has systematically compared the performance of cfDNA and cfRNA co-purification to increase sensitivity.

RESULTS

First, we set up a framework using digital PCR (dPCR) technology to quantify cfDNA and cfRNA from human blood plasma in order to compare cfDNA/cfRNA co-purification kit performance. To that end, we optimized two dPCR duplex assays, designed to quantify both cfDNA and cfRNA with the same assays, by ensuring that primers and probes are located within a highly abundant exon. Next, we applied our optimized workflow to evaluate the co-purification performance of two manual and two semi-automated methods over a range of plasma input volumes (0.06-4 mL). Some kits result in higher nucleic acid concentrations in the eluate, while consuming only half of the plasma volume. The combined nucleic acid quantification systematically results in higher nucleic acid concentrations as compared to a parallel quantification of cfDNA and cfRNA in the eluate.

CONCLUSIONS

We provide a framework to evaluate the performance of cfDNA/cfRNA co-purification kits and have tested two manual and two semi-automated co-purification kits in function of the available plasma input amount and the intended use of the nucleic acid eluate. We demonstrate that the combined quantification of cfDNA and cfRNA has a benefit compared to separate quantification. We foresee that the results of this study are instrumental for clinical applications to help increase mutation detection sensitivity, allowing improved disease detection and monitoring.

Low-temperature co-purification of NOx and Hg0 from simulated flue gas by CexZryMnzO2/r-Al2O3: the performance and its mechanism

In this study, series of Ce_xZr_yMn_zO₂/r-Al₂O₃ catalysts were prepared by impregnation method and explored to co-purification of NO_x and Hg⁰ at low temperature. The physical and chemical properties of the catalysts were investigated by XRD, BET, FTIR, NH₃-TPD, H₂-TPR, and XPS. The experimental results showed that 10% Ce_0.2Zr_0.3Mn_0.5O₂/r-Al₂O₃ yielded higher conversion on co-purification of NO_x and Hg⁰ than the other prepared catalysts at low temperature, especially at 200-300 °C. 91% and 97% convert rate of NO_x and Hg⁰ were obtained, respectively, when 10% Ce_0.2Zr_0.3Mn_0.5O₂/r-Al₂O₃ catalyst was used at 250 °C. Moreover, the presence of H₂O slightly decreased the removal of NO_x and Hg⁰ owing to the competitive adsorption of H₂O and Hg⁰. When SO₂ was added, the removal of Hg⁰ first increased slightly and then presented a decrease due to the generation of SO₃ and (NH₄)₂SO₄. The results of NH₃-TPD indicated that the strong acid of 10% Ce_0.2Zr_0.3Mn_0.5O₂/r-Al₂O₃ improved its high-temperature activity. XPS and H₂-TPR results showed there were high-valence Mn and Ce species in 10% Ce_0.2Zr_0.3Mn_0.5O₂/r-Al₂O₃, which could effectively promote the removal of NO_x and Hg⁰. Therefore, the mechanisms of Hg⁰ and NO_x removal were proposed as Hg (ad) + [O] → HgO (ad), and 2NH₃/NH₄⁺ (ad) + NO₂ (ad) + NO (g) → 2 N₂ + 3H₂O/2H⁺, respectively. Graphical abstract ᅟ.