Biophysical Studies of Asymmetric Homodimerisation of the microRNA Biogenesis Cofactors PACT and TRBP

Processing of precursor microRNAs by Dicer is a key step in microRNA biogenesis. This process is assisted by the homologous proteins PACT and TRBP, which bind to the helicase domain of Dicer. The mechanism by which they assist microRNA biogenesis is poorly understood, but could include facilitating substrate positioning, assisting Argonaute loading, or discriminating between different classes of pre-miRNA. PACT also regulates innate immune pathways that respond to viral double-stranded RNA, including via the kinase PKR. Mutations in PACT lead to early onset dystonia in humans, while depletion of PACT in mice results in both growth and fertility defects: both have been linked to inappropriate or altered activation of PKR. Homodimerisation of PACT via its C-terminal domain (PACT-D3) is thought to be necessary for it to induce PKR activation. Homodimerisation of wild-type and mutant constructs of PACT-D3 was assayed using biophysical techniques. SEC-MALLS and analytical ultracentrifugation data demonstrate that PACT-D3 homodimerises via a different mechanism to a previously reported dsRBD homodimer, dsRBD-5 of Staufen1. Instead, NMR analyses show that PACT-D3 forms an asymmetric homodimer similar to that observed in the Drosophila melanogaster homologue Loquacious. Dimerisation could be abolished by the L273R mutation, while phospho-mimic mutations did not appear to significantly affect dimerisation. TRBP domain 3 also forms asymmetric dimers, but with weaker affinity due to sequence differences in its C- terminal -helix. Asymmetry is caused by a register shift between intermolecular parallel beta-strands, but the functional significance of asymmetric homodimerisation remains unclear. The data presented in this thesis supports a model in which the homodimerisation interface of PACT-D3 overlaps with the surface that binds to Dicer, and suggests that PACT homodimerisation and the formation of a Dicer-PACT complex are incompatible

Correction to : 1H, 13C, 15N backbone and IVL methyl group resonance assignment of the fungal β-glucosidase from Trichoderma reesei (Biomolecular NMR Assignments, (2020), 10.1007/s12104-020-09959-2)

In the original publication of the article, the name of one of the authors is incorrect. The author's name is Eiso AB, but was modified to A. B. Eiso. The correct name is given in this Correction

1H, 13C, 15N backbone and IVL methyl group resonance assignment of the fungal β-glucosidase from Trichoderma reesei

β-glucosidases have received considerable attention due to their essential role in bioethanol production from lignocellulosic biomass. β-glucosidase can hydrolyse cellobiose in cellulose degradation and its low activity has been considered as one of the main limiting steps in the process. Large-scale conversions of cellulose therefore require high enzyme concentration which increases the cost. β-glucosidases with improved activity and thermostability are therefore of great commercial interest. The fungus Trichoderma reseei expresses thermostable cellulolytic enzymes which have been widely studied as attractive targets for industrial applications. Genetically modified β-glucosidases from Trichoderma reseei have been recently commercialised. We have developed an approach in which screening of low molecular weight molecules (fragments) identifies compounds that increase enzyme activity and are currently characterizing fragment-based activators of TrBgl2. A structural analysis of the 55 kDa apo form of TrBgl2 revealed a classical (α/β)8-TIM barrel fold. In the present study we present a partial assignment of backbone chemical shifts, along with those of the Ile (I)-Val (V)-Leu (L) methyl groups of TrBgl2. These data will be used to characterize the interaction of TrBgl2 with the small molecule activators

S6K2-mediated regulation of TRBP as a determinant of miRNA expression in human primary lymphatic endothelial cells

MicroRNAs (miRNAs) are short non-coding RNAs that silence mRNAs. They are generated following transcription and cleavage by the DROSHA/DGCR8 and DICER/TRBP/PACT complexes. Although it is known that components of the miRNA biogenesis machinery can be phosphorylated, it remains poorly understood how these events become engaged during physiological cellular activation. We demonstrate that S6 kinases can phosphorylate the extended C-terminal domain of TRBP and interact with TRBP in situ in primary cells. TRBP serines 283/286 are essential for S6K-mediated TRBP phosphorylation, optimal expression of TRBP, and the S6K-TRBP interaction in human primary cells. We demonstrate the functional relevance of this interaction in primary human dermal lymphatic endothelial cells (HDLECs). Angiopoietin-1 (ANG1) can augment miRNA biogenesis in HDLECs through enhancing TRBP phosphorylation and expression in an S6K2-dependent manner. We propose that the S6K2/TRBP node controls miRNA biogenesis in HDLECs and provides a molecular link between the mTOR pathway and the miRNA biogenesis machinery

Silver–N-heterocyclic carbenes in π–Activation: Synergistic effects between the ligand ring size and the anion

A series of 12 silver­(I)–N-heterocyclic carbene (NHC) complexes were prepared featuring five- (both saturated and unsaturated backbone), six-, and seven-membered ring ligand scaffolds. The N-substituents of the NHCs were diisopropylphenyl in all cases, while the anion was varied between bromide, acetate, and triflate. The complexes were evaluated as catalysts in the spirocyclization of 1-(1H-indol-3-yl)-4-phenylbut-3-yn-2-one to give a spirocyclic indolenine product. To our knowledge, it is the first time that a systematic study has been conducted to examine the effects of both NHC ring size and anion in this type of silver-catalyzed reaction. While the acetate and triflate complexes catalyzed the reaction to 100% conversion, the bromide complexes exhibited a significant ligand/anion effect. Reactions catalyzed by both complexes bearing the five-membered ring NHC ligands and the complex bearing the seven-membered ring NHC ligand stalled after approximately two turnovers. However, the bromide complex bearing the six-membered ring NHC ligand catalyzes the reaction to almost full conversion, similarly to the acetate and triflate complexes. This demonstrates that the NHC ligand ring size can have a dramatic effect in these types of reactions and does not necessarily display a linear correlation

A Reductive Aminase Switches to Imine Reductase Mode for a Bulky Amine Substrate

Imine Reductases (IREDs) catalyze the asymmetric reduction of cyclic imines, but also in some cases the coupling of ketones and amines to form secondary amine products in an enzyme-catalyzed reductive amination (RedAm) reaction. Enzymatic RedAm reactions have typically used small hydrophobic amines, but many interesting pharmaceutical targets require that larger amines are used in these coupling reactions. Following the identification of IR77 from Ensifer adhaerens as a promising biocatalyst for the reductive amination of cyclohexanone with pyrrolidine, we have characterized the ability of this enzyme to catalyze couplings with larger bicyclic amines such as isoindoline and octahydrocyclopenta(c)pyrrole. By comparing the activity of IR77 with reductions using sodium cyanoborohydride in water, it was shown that, while the coupling of cyclohexanone and pyrrolidine involved at least some element of reductive amination, the amination with the larger amines likely occurred ex situ, with the imine recruited from solution for enzyme reduction. The structure of IR77 was determined and using this as a basis, structure-guided mutagenesis, coupled with point mutations selecting improving amino acid sites suggested by other groups, permitted the identification of a mutant A208N with improved activity for amine product formation. Improvements in conversion were attributed to greater enzyme stability as revealed by X-ray crystallography and nano differential scanning fluorimetry. The mutant IR77-A208N was applied to the preparative scale amination of cyclohexanone at 50 mM concentration, with 1.2 equivalents of three larger amines, in isolated yields of up to 93%

Conserved asymmetry underpins homodimerization of Dicer-associated double-stranded RNA-binding proteins

Double-stranded RNA-binding domains (dsRBDs) are commonly found in modular proteins that interact with RNA. Two varieties of dsRBD exist: canonical Type A dsRBDs interact with dsRNA, while non-canonical Type B dsRBDs lack RNA-binding residues and instead interact with other proteins. In higher eukaryotes, the microRNA biogenesis enzyme Dicer forms a 1:1 association with a dsRNA-binding protein (dsRBP). Human Dicer associates with HIV TAR RNA-binding protein (TRBP) or protein activator of PKR (PACT), while Drosophila Dicer-1 associates with Loquacious (Loqs). In each case, the interaction involves a region of the protein that contains a Type B dsRBD. All three dsRBPs are reported to homodimerize, with the Dicer-binding region implicated in self-association. We report that these dsRBD homodimers display structural asymmetry and that this unusual self-association mechanism is conserved from flies to humans. We show that the core dsRBD is sufficient for homodimerization and that mutation of a conserved leucine residue abolishes self-association. We attribute differences in the self-association properties of Loqs, TRBP and PACT to divergence of the composition of the homodimerization interface. Modifications that make TRBP more like PACT enhance self-association. These data are examined in the context of miRNA biogenesis and the protein/protein interaction properties of Type B dsRBDs

CCDC 2064124 - 2064130: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures

SARS-CoV-2 vaccination modelling for safe surgery to save lives: data from an international prospective cohort study

Background: Preoperative SARS-CoV-2 vaccination could support safer elective surgery. Vaccine numbers are limited so this study aimed to inform their prioritization by modelling. Methods: The primary outcome was the number needed to vaccinate (NNV) to prevent one COVID-19-related death in 1 year. NNVs were based on postoperative SARS-CoV-2 rates and mortality in an international cohort study (surgical patients), and community SARS-CoV-2 incidence and case fatality data (general population). NNV estimates were stratified by age (18-49, 50-69, 70 or more years) and type of surgery. Best- and worst-case scenarios were used to describe uncertainty. Results: NNVs were more favourable in surgical patients than the general population. The most favourable NNVs were in patients aged 70 years or more needing cancer surgery (351; best case 196, worst case 816) or non-cancer surgery (733; best case 407, worst case 1664). Both exceeded the NNV in the general population (1840; best case 1196, worst case 3066). NNVs for surgical patients remained favourable at a range of SARS-CoV-2 incidence rates in sensitivity analysis modelling. Globally, prioritizing preoperative vaccination of patients needing elective surgery ahead of the general population could prevent an additional 58 687 (best case 115 007, worst case 20 177) COVID-19-related deaths in 1 year. Conclusion: As global roll out of SARS-CoV-2 vaccination proceeds, patients needing elective surgery should be prioritized ahead of the general population