The 3' UTR of vigR is required for virulence in Staphylococcus aureus and has expanded through STAR sequence repeat insertions.

Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are alarmingly common, and treatment is confined to last-line antibiotics. Vancomycin is the treatment of choice for MRSA bacteremia, and treatment failure is often associated with vancomycin-intermediate S. aureus isolates. The regulatory 3' UTR of the vigR mRNA contributes to vancomycin tolerance and upregulates the autolysin IsaA. Using MS2-affinity purification coupled with RNA sequencing, we find that the vigR 3' UTR also regulates dapE, a succinyl-diaminopimelate desuccinylase required for lysine and peptidoglycan synthesis, suggesting a broader role in controlling cell wall metabolism and vancomycin tolerance. Deletion of the 3' UTR increased virulence, while the isaA mutant is completely attenuated in a wax moth larvae model. Sequence and structural analyses of vigR indicated that the 3' UTR has expanded through the acquisition of Staphylococcus aureus repeat insertions that contribute sequence for the isaA interaction seed and may functionalize the 3' UTR.

Molecular dynamic simulations of diacridine binding to DNA: Indications that C6 diacridine can bisintercalate spanning two base pairs.

Dimers of 9-aminoacridine linked via the 9-amino group with polymethylene chains, termed diacridines, are known to bisintercalate into DNA when the linker comprises 6 or more methylene units. There are no literature reports of crystal or NMR solution structures for bisintercalated diacridine-DNA complexes, and the issue of the structure of the C6 ([CH2 ]n linker where n = 6) diacridine complex remains unresolved. Previously, based on simple geometric considerations, it was proposed that C6 diacridine could only span a single base pair, which requires that its bifunctional reaction violates the widely-observed "neighbor exclusion principle" where bound intercalators are separated by at least 2 base pairs. Here we have explored the structure of diacridine-DNA complexes using unrestrained molecular dynamics in explicit solvent using the parmbsc0 forcefield in AMBER14. We studied the C4 to C8 dimers, intercalated via both the minor and major DNA grooves, to a variety of nucleotide sequences. We find that C6, C7, and C8 diacridine are able to form 2 base pair bisintercalated complexes from either groove, whereas the C4 and C5 homologues cannot. We conclude that C6 diacridine does have the capacity to bisintercalate without violating neighbor exclusion, and that the previous proposed binding model needs revision.

Structural Effects on the Norrish Type I α-Bond Cleavage of Tropospherically Important Carbonyls.

Norrish Type I (NTI) α-bond cleavage is the dominant photolysis mechanism in small carbonyls and is an important source of radicals in the troposphere. In nonsymmetric species two cleavages are possible, NTIa and NTIb, forming larger and smaller alkyl radicals, respectively. For a data set of 20 small, atmospherically relevant carbonyls we predict NTIa and NTIb thresholds on the S0, S1, and T1 electronic states. The calculated NTIa T1 thresholds give a mean absolute deviation (MAD) of 5.8 kJ/mol with respect to the available experimental thresholds of five carbonyls. In addition, the intrinsic barrier heights to dissociation on the S0, S1, and T1 electronic states are predicted. We find RI-B2GP-PLYP/def2-TZVP calculations on S0 and unrestricted RI-B2GP-PLYP/def2-TZVP calculations on T1 give MADs of 6.1 kJ/mol for S0 asymptotic energies and 6.3 kJ/mol for S0 → T1 0-0 excitation energies, with respect to available experimental data. A composite method is used to determine S1 thresholds, with bt-STEOM-CCSD/cc-pVQZ calculation of vertical excitation energies and TD-RI-B3LYP/def2-TZVP calculations on S1, which achieves a MAD of 7.2 kJ/mol, with respect to experimental 0-0 excitation energies. Our calculations suggest, with the exception of bifunctional carbonyls and enones, NTI reactions on S1 are unlikely to be important at tropospherically relevant photolysis energies (<400 kJ/mol). In contrast, at these energies almost all possible NTI channels on T1 are open, and all barrierless S0 NTI dissociations are accessible. Our calculations allow a number of structural effects on both 0-0 excitation energies and intrinsic reaction barriers, on a given electronic state, to be elucidated and rationalized.

Dynamics and quantum yields of H2 + CH2CO as a primary photolysis channel in CH3CHO.

The first experimental observation of the primary photochemical channel of acetaldehyde leading to the formation of ketene (CH2CO) and hydrogen (H2) molecular products is reported. Acetaldehyde (CH3CHO) was photolysed in a molecular beam at 305.6 nm and the resulting H2 product characterized using velocity-map ion (VMI) imaging. Resonance-enhanced multiphoton ionization (REMPI), via two-photon excitation to the double-well EF 1Σ state, was used to state-selectively ionize the H2 and determine angular momentum distributions for H2 (ν = 0) and H2 (ν = 1). Velocity-map ion images were obtained for H2 (ν = 0 and 1, J = 5), allowing the total translational energy release of the photodissociation process to be determined. Following photolysis of CH3CHO in a gas cell, the CH2CO co-fragment was identified, using Fourier transform infrared spectroscopy, by its characteristic infrared absorption at 2150 cm-1. The measured quantum yield of the CH2CO + H2 product channel at 305.0 nm is φ = 0.0075 ± 0.0025 for both 15 Torr of neat CH3CHO and a mixture with 745 Torr of N2. Although small, this result has implications for the atmospheric photochemistry of carbonyls and this reaction represents a new tropospheric source of H2. Quasi-classical trajectory (QCT) simulations on a zero-point energy corrected reaction-path potential are also performed. The experimental REMPI and VMI image distributions are not consistent with the QCT simulations, indicating a non reaction-path mechanism should be considered.