Role of the trigger loop in translesion RNA synthesis by bacterial RNA polymerase

DNA lesions can severely compromise transcription and block RNA synthesis by RNA polymerase (RNAP), leading to subsequent recruitment of DNA repair factors to the stalled transcription complex. Recent structural studies have uncovered molecular interactions of several DNA lesions within the transcription elongation complex. However, little is known about the role of key elements of the RNAP active site in translesion transcription. Here, using recombinantly expressed proteins,in vitrotranscription, kinetic analyses, andin vivocell viability assays, we report that point amino acid substitutions in the trigger loop, a flexible element of the active site involved in nucleotide addition, can stimulate translesion RNA synthesis byEscherichia coliRNAP without altering the fidelity of nucleotide incorporation. We show that these substitutions also decrease transcriptional pausing and strongly affect the nucleotide addition cycle of RNAP by increasing the rate of nucleotide addition but also decreasing the rate of translocation. The secondary channel factors DksA and GreA modulated translesion transcription by RNAP, depending on changes in the trigger loop structure. We observed that although the mutant RNAPs stimulate translesion synthesis, their expression is toxicin vivo, especially under stress conditions. We conclude that the efficiency of translesion transcription can be significantly modulated by mutations affecting the conformational dynamics of the active site of RNAP, with potential effects on cellular stress responses and survival

Adsorption of Glyoxal (CHOCHO) and Its UV Photolysis Products on the Surface of Atmospheric Ice Nanoparticles. DFT and Density Functional Tight-Binding Study

The structures, energies, harmonic vibrational frequencies, and thermodynamic parameters of the water clusters (H2O)48, (H2O)72, and (H2O)270 were calculated using the standard DFT theory (BLYP/6-31++G(d,p) for small and medium clusters) and the modern tight-binding method SCC-DFTB (DFTBA and DFTB+). The adsorption and embedding of s-cis- and s-trans-glyoxal molecules as well as its sunlight UV photolysis products (molecules CH2O, HCOOH, H2O2, CO, CO2 and radicals CHO, HO, HO2) on nanosized ice clusters of up to 2.5 nm in diameter were studied within the above theoretical models. The structures of adsorption complexes on different sites of ice nanoparticles, the corresponding adsorption energies and thermodynamic parameters were estimated. We found that the DFTB method is a very promising tool for the calculations of structures and energies of ice nanoparticles, when compared to both DFT and semiempirical (PM3) methods. The obtained results are discussed in relation to the possible photolysis pathways, the reaction rates in the gas phase and in the adsorbed state, and the mechanisms of glyoxal photolysis catalyzed by the ice nanoparticles in the Earth’s atmosphere

Pb₂MnTeO₆ Double Perovskite: An Antipolar Anti-ferromagnet

Pb₂MnTeO₆, a new double perovskite, was synthesized. Its crystal structure was determined by synchrotron X-ray and powder neutron diffraction. Pb₂MnTeO₆ is monoclinic (<i>I</i>2/<i>m</i>) at room temperature with a regular arrangement of all the cations in their polyhedra. However, when the temperature is lowered to ∼120 K it undergoes a phase transition from <i>I</i>2/<i>m</i> to <i>C</i>2/<i>c</i> structure. This transition is accompanied by a displacement of the Pb atoms from the center of their polyhedra due to the 6s² lone-pair electrons, together with a surprising off-centering of Mn²⁺ (d⁵) magnetic cations. This strong first-order phase transition is also evidenced by specific heat, dielectric, Raman, and infrared spectroscopy measurements. The magnetic characterizations indicate an anti-ferromagnetic (AFM) order below <i>T</i>_N ≈ 20 K; analysis of powder neutron diffraction data confirms the magnetic structure with propagation vector <i>k</i> = (0 1 0) and collinear AFM spins. The observed jump in dielectric permittivity near ∼150 K implies possible anti-ferroelectric behavior; however, the absence of switching suggests that Pb₂MnTeO₆ can only be antipolar. First-principle calculations confirmed that the crystal and magnetic structures determined are locally stable and that anti-ferroelectric switching is unlikely to be observed in Pb₂MnTeO₆