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DNA scaffolds enable the activation and suppression of photochemistry between strongly-coupled synthetic chromophores.
The XRCC1–DNA ligase IIIα complex (XL) is critical for DNA single-strand break repair, a key target for PARP inhibitors in cancer cells deficient in homologous recombination. Here, we combined biophysical approaches to gain insights into the shape and conformational flexibility of the XL as well as XRCC1 and DNA ligase IIIα (LigIIIα) alone. Structurally-guided mutational analyses based on the crystal structure of the human BRCT–BRCT heterodimer identified the network of salt bridges that together with the N-terminal extension of the XRCC1 C-terminal BRCT domain constitute the XL molecular interface. Coupling size exclusion chromatography with small angle X-ray scattering and multiangle light scattering (SEC-SAXS–MALS), we determined that the XL is more compact than either XRCC1 or LigIIIα, both of which form transient homodimers and are highly disordered. The reduced disorder and flexibility allowed us to build models of XL particles visualized by negative stain electron microscopy that predict close spatial organization between the LigIIIα catalytic core and both BRCT domains of XRCC1. Together our results identify an atypical BRCT–BRCT interaction as the stable nucleating core of the XL that links the flexible nick sensing and catalytic domains of LigIIIα to other protein partners of the flexible XRCC1 scaffold.
The evolution of eukaryotic lipid-bound organelles allows for specialized metabolism to occur within spatially distinct metabolic landscapes within the same cell. However, this strategy of compartmentalization is not unique to eukaryotic organisms. Many bacteria, spread across 45 different phyla, contain loci that encode for specialized bacterial microcompartments (BMCs) (Sutter et al., 2021). The formation of a BMC involves self-assembly from three families of shell proteins to form the outer shell membrane, in addition to the encapsulation of an enzymatic core packaged within the lumen of a BMC (Kerfeld et al., 2018). These proteinaceous organelles provide a competitive growth advantage by enabling organisms to process inaccessible substrates by sequestering metabolic intermediates (i.e. aldehydes) that would otherwise be toxic within the cytoplasm. While BMCs perform specific metabolic functions in their native organism, synthetic, empty BMC shells can form without the requirement of native cargo inside (Doron and Kerfeld, 2024). This provides a transferable and tunable platform of protein scaffolding for guiding metabolic engineering within a host organism of choice (Raba and Kerfeld, 2022).
The excitation of carbonyl compounds by light to generate radical intermediates has historically been restricted to ketones and aldehydes; carboxylic acids have been overlooked because of high energy requirements and low quantum efficiency. A successful activation strategy would necessitate a bathochromic shift in the absorbance profile, an increase in triplet diradical lifetime, and ease of further functionalization. We present a single-flask transformation of carboxylic acids to acyl phosphonates that can access synthetically useful triplet diradicals under visible light or near-ultraviolet irradiation. The use of phosphorus circumvents unproductive Norrish type I processes, promoting selectivity that enables hydrogen-atom transfer reactivity. Use of this strategy promotes the efficient scaffold remodeling of carboxylic acids through various annulation, contraction, and expansion manifolds.
The synthesis of exopolysaccharides as biofilm matrix components by pathogens is a crucial factor for chronic infections and antibiotic resistance. Many periplasmic proteins involved in polymer processing and secretion in Gram-negative synthase dependent exopolysaccharide biosynthetic systems have been individually characterized. The operons responsible for the production of PNAG, alginate, cellulose and the Pel polysaccharide each contain a gene that encodes an outer membrane associated tetratricopeptide repeat (TPR) domain containing protein. While the TPR domain has been shown to bind other periplasmic proteins, the functional consequences of these interactions for the polymer remain poorly understood. Herein, we show that the C-terminal TPR region of PgaA interacts with the de-N-acetylase domain of PgaB, and increases its deacetylase activity. Additionally, we found that when the two proteins form a complex, the glycoside hydrolase activity of PgaB is also increased. To better understand structure-function relationships we determined the crystal structure of a stable TPR module, which has a conserved groove formed by three repeat motifs. Tryptophan quenching, mass spectrometry analysis and molecular dynamics simulation studies suggest that the crystallized TPR module can bind PNAG/dPNAG via its electronegative groove on the concave surface, and potentially guide the polymer through the periplasm towards the porin for export. Our results suggest a scaffolding role for the TPR domain that combines PNAG/dPNAG translocation with the modulation of its chemical structure by PgaB.
The concern over greenhouse gases, methane (CH 4 ) and carbon dioxide (CO 2 ), is increasing rapidly. There have been strides to find solutions to this global issue but there is not a clear path to a successful end goal. The concentration of CH 4 and CO 2 in the atmosphere has increased significantly over the last 60 years, methane is a great source of concern due to its ability to trap a high amount of heat in the atmosphere. These greenhouse gases contribute to global warming which has caused changes in the environment, including the melting of ice caps, and altered weather patterns. Solutions for these pressing challenges have led to different avenues of methane mitigation one of which is the development of solid-state bioreactors. These reactors harness the power of biological species that have evolved to use methane as an energy source. The development and optimization of Hollow Scaffold Solid State Bioreactors (HS-SSBR) has become readily available due to the advancements in additive manufacturing technology and accessibility of computer aided design (CAD) software. With laboratory scale experiments, time and effort are of great importance. Enhancing the design of the HS-SSBR to create a more user-friendly interface, but also increase the functionality of the reactor. The reactor's design improvements focus on better dispersion of methane and circulation of media.
As part of free cellulases or scaffolding proteins in cellulosomes, the hydrophilic non-catalytic X2 module is widely distributed in cellulolytic Clostridia or other Firmicutes bacteria. Previous biochemical studies suggest that X2 modules might increase the solubility and substrate binding affinity of X2-bearing proteins. However, their in vivo biological functions remain elusive. Here we employed CRISPR-Cas9 editing to genetically modify X2 modules by deleting the conserved motif (NGNT) from the CipC scaffoldin. Both single and double X2 mutants (X2-N: near the N terminus of CipC; X2-C: near the C terminus of CipC) presented similar stoichiometric compositions in isolated cellulosomes as the wildtype strain (WT). These X2 mutants had an elongated adaptation stage during growth on cellulose compared to cellobiose. Compared to WT, the double mutant ΔX2-NC reduced cellulose degradation by 15% and the amount of released soluble sugars by 63%. Since single X2 mutants did not present such obvious physiological changes as ΔX2-NC, there seems to be a functional redundancy between X2 modules in CipC. The in vivo adhesion assay revealed that ΔX2-NC decreased cell attachment to cellulose by 70% but a weaker effect was also overserved in single X2 mutants. These results highlight the in vivo biological role of X2 in increasing cellulose degradation efficiency by enhancing the binding affinity between cells and cellulose, which provides new perspectives for microbial engineering.
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For hydrogen storage materials to become practically viable, comprehensive improvements in key properties—kinetics, thermodynamics, thermal transport, and durability—are crucial. Porous Mg structure has been proposed as a promising strategy due to its high storage capacity and ability to accommodate volume expansion. However, challenges such as sluggish kinetics and structural degradation resulting from instability due to vacant sites still remain. In this study, a tailored design of porous Mg structure with site-specific transition metal dual-doping and structure-reinforced carbon nanotube (CNT)-framework is presented for optimal hydrogen storage. Ti and Ni are strategically deposited on the surface to synergistically enhance hydrogen sorption kinetics by facilitating hydrogen dissociation and diffusion, while CNTs are interpenetrated into 3D Mg structure for improving thermal conductivity and maintaining the porous structure. The resulting composite demonstrates exceptional performance, achieving hydrogen absorption and desorption of 4.8 and 5.8 wt%, respectively, within 10 min with an impressively low activation energy for absorption of 46 kJ mol −1 H 2 . Even after 50 cycles, its capacity and porous structure are well preserved, showing excellent cyclability in comparison with previously reported materials. In conclusion, this delicate design strategy based on a comprehensive understanding of structural and chemical characteristics is key to maximizing the targeted performance.
Abstract NifEN plays a crucial role in the biosynthesis of nitrogenase, catalyzing the final step of cofactor maturation prior to delivering the cofactor to NifDK, the catalytic component of nitrogenase. The difficulty in expressing NifEN, a complex, heteromultimeric metalloprotein sharing structural/functional homology with NifDK, is a major challenge in the heterologous expression of nitrogenase. Herein, we report the expression and engineering of Azotobacter vinelandii NifEN in Escherichia coli . Biochemical and spectroscopic analyses demonstrate the integrity of the heterologously expressed NifEN in composition and functionality and, additionally, the ability of an engineered NifEN variant to mimic NifDK in retaining the matured cofactor at an analogous cofactor‐binding site. This is an important step toward piecing together a viable pathway for the heterologous expression of nitrogenase and identifying variants for the mechanistic investigation of this enzyme.
NifEN plays a crucial role in the biosynthesis of nitrogenase, catalyzing the final step of cofactor maturation prior to delivering the cofactor to NifDK, the catalytic component of nitrogenase. The difficulty in expressing NifEN, a complex, heteromultimeric metalloprotein sharing structural/functional homology with NifDK, is a major challenge in the heterologous expression of nitrogenase. Herein, we report the expression and engineering of Azotobacter vinelandii NifEN in Escherichia coli. Biochemical and spectroscopic analyses demonstrate the integrity of the heterologously expressed NifEN in composition and functionality and, additionally, the ability of an engineered NifEN variant to mimic NifDK in retaining the matured cofactor at an analogous cofactor-binding site. This is an important step toward piecing together a viable pathway for the heterologous expression of nitrogenase and identifying variants for the mechanistic investigation of this enzyme.
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Glass, a near infinitely recyclable material, can be upcycled to create new products such as foamed glass ceramics, which are essentially a synthetic pumice-like material. This material has been demonstrated to sustain preserved biofilms which have application in various fields based on the deployability of the product and the preserved microbes. Foamed glass ceramics have increased surface area compared to typical soda-lime glass cullet. This material has been explored for variety of applications including the growth, storage and transport of biofilms and microbial colonies which can be preserved and deployed later. Here, we demonstrate the ability for microbial cultures including BioTiger™, Escherichia coli K-12, Bacillus thuringiensis, and two environmental eukaryotic cells to colonize the upcycled glass products, undergo preservation, and regrow after 84 days of storage. The growth of preserved samples is correlated to the time spent incubating prior to preservation. These results demonstrate the applicability of this novel glass-biofilm combination in which various preserved microorganisms are able to be rapidly grown after storage on an upcycled glass product.
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