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Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs
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Microwave-Based Synthesis of Functional Morphological Variants and Carbon Nanotube-Based Composites of VS 4 for Electrochemical Applications
A novel facile, fast, and efficient microwave-assisted method was developed to synthesize a number of diverse nanostructured motifs (ranging from nanorods to nanoflowers) of VS 4 along with its associated composite heterostructures, VS 4 /multi-walled carbon nanotube (MWNT; i.e., multi-walled carbon nanotubes). Specifically, we have probed and correlated the effects of a number of specific experimental variables, including primarily precursor, solvent, temperature, and time. We noted that nanorods formed more readily with VO(acac) 2 as the vanadium precursor and n-methyl-2-pyrrolidone (NMP) as a polar reaction solvent. By contrast, we determined that hierarchical three-dimensional (3D) nanoflower-like assemblies, ranging in size from 100 to 200 nm in average diameter, could be controllably synthesized by using Na 3 VO 4 as the vanadium precursor and an aqueous water: polar solvent mixture as the reaction medium. We also observed that VS 4 disintegrates, when in the presence of either air, solution, or a combination of these environments, and established that the extent of VS4 nanorod decomposition could be almost fully prevented by storage under nitrogen. From an application’s perspective, our VS 4 is electrochemically active and shows behavior, consistent with the literature. In particular, as compared with pristine VS 4 nanorods alone, we observed enhanced electrochemical activity with (i) 3D hierarchical flower-like motifs, (ii) unique necklace-like VS 4 nanorod–MWNT composites, and (iii) samples in which as-prepared VS4 nanorods had been annealed. Moreover, we found that the rational application of specific physical and chemical processing treatments, such as (i) thermal annealing to improve crystallinity, (ii) the addition of MWNTs to form conductive composites, and (iii) the evolution of morphology from one-dimensional (1D) nanorods to more complex 3D nanoflowers, was favorable to the resulting electrochemical performance with respect to increasing stability and reversibility.
Thermostable Enzyme Variants in the Lower Mevalonate Pathway Improve Isoprenoid Production by Cell-Free Biocatalysis
Cell-free biocatalysis is a rapidly evolving field with great potential for sustainably producing valuable chemicals. Some challenges in cell-free biocatalysis include reaction longevity, enzyme stability, and the cost of the biocatalysts. Here, the challenge of enzyme instability was addressed by employing thermophilic enzymes to improve the productivity of the lower mevalonate pathway, using limonene as an example isoprenoid product. The Classical mesophilic mevalonate pathway was compared to a newly assembled set of thermophilic enzymes comprising the Archaea I mevalonate pathway. The thermophilic pathway enzymes were thermostable to at least 60 °C and exhibited a 6× longer operating lifetime at 22 °C. Thus, despite lower initial activity rates at ambient temperature, the thermophilic pathway was longer-lived and resulted in a more productive cell-free reaction overall, achieving 1.7× higher yield of limonene compared to using enzymes from mesophiles. Moreover, the thermostable pathway retained activity for longer with the challenge of solvent exposure, namely, ethanol and isoprenol, which broadens the scope of accessible substrates and/or products in cell-free reactions employing this pathway. Altogether, we showed significant improvement in the stability and productivity of the lower mevalonate pathway, which will enable more efficient cell-free biosynthesis of isoprenoid products. This represents a valuable strategy to increase the robustness of cell-free systems by carefully sourcing biocatalysts from thermophilic organisms, which have proven to be resilient to challenges unique to cell-free reaction systems.
Fast Determination of the Lignin Monomer Compositions of Genetic Variants of Poplar via Fast Pyrolysis/Atmospheric Pressure Chemical Ionization Mass Spectrometry
Not provided.
Macroecological distributions of gene variants highlight the functional organization of soil microbial systems
Abstract The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.
Identification of functional non-coding variants associated with orofacial cleft
Oral facial cleft (OFC) comprises cleft lip with or without cleft palate (CL/P) or cleft palate only. Genome wide association studies (GWAS) of isolated OFC have identified common single nucleotide polymorphisms (SNPs) in many genomic loci where the presumed effector gene (for example, IRF6 in the 1q32 locus) is expressed in embryonic oral epithelium. To identify candidates for functional SNPs at eight such loci we conduct a massively parallel reporter assay in a fetal oral epithelial cell line, revealing SNPs with allele-specific effects on enhancer activity. We filter these SNPs against chromatin-mark evidence of enhancers and test a subset in traditional reporter assays, which support the candidacy of SNPs at loci containing FOXE1, IRF6, MAFB, TFAP2A, and TP63. For two SNPs near IRF6 and one near FOXE1, we engineer the genome of induced pluripotent stem cells, differentiate the cells into embryonic oral epithelium, and discover allele-specific effects on the levels of effector gene expression, and, in two cases, the binding affinity of transcription factors FOXE1 or ETS2. Conditional analyses of GWAS data suggest the two functional SNPs near IRF6 account for the majority of risk for CL/P at this locus. This study connects genetic variation associated with OFC to mechanisms of pathogenesis.
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail
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Fast and efficient template-mediated synthesis of genetic variants
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Characterization of an unusual SARS-CoV-2 main protease natural variant exhibiting resistance to nirmatrelvir and ensitrelvir
We investigate the effects of two naturally selected substitution and deletion (Δ) mutations, constituting part of the substrate binding subsites S2 and S4, on the structure, function, and inhibition of SARS CoV-2 main protease. Comparable to wild-type, MPro D48Y/ΔP168 undergoes N-terminal autoprocessing essential for stable dimer formation and mature-like catalytic activity. The structures are similar, but for an open active site conformation in MPro D48Y/ΔP168 and increased dynamics of the S2 helix, S5 loop, and the helical domain. Some dimer interface contacts exhibit shorter H bond distances corroborating the ~40-fold enhanced dimerization of the mutant although its thermal sensitivity to unfolding is 8 °C lower, relative to wild-type. ITC reveals a 3- and 5-fold decrease in binding affinity for nirmatrelvir and ensitrelvir, respectively, and similar GC373 affinity, to MPro D48Y/ΔP168 relative to wild-type. Structural differences in four inhibitor complexes of MPro D48Y/ΔP168 compared to wild-type are described. Consistent with enhanced dynamics, the S2 helix and S5 loop adopting a more open conformation appears to be a unique feature of MPro D48Y/ΔP168 both in the inhibitor-free and bound states. Our results suggest that mutational effects are compensated by changes in the conformational dynamics and thereby modulate N-terminal autoprocessing, K dimer , catalytic efficiency, and inhibitor binding.
Kinetics of cooperative CO2 adsorption in diamine-appended variants of the metal–organic framework Mg2(dobpdc)
An in-depth investigation of the CO 2 adsorption kinetics of a promising class of cooperative carbon capture materials offers new insight into their structure-performance properties.
Understanding CO 2 adsorption on the surfaces of SrO and its hydroxylated variants Sr(OH) 2 · n H 2 O ( n = 0, 1, 8)
Strontium oxide (SrO) is a promising material for CO 2 capture through a reversible cycle of carbonation and calcination, where SrO reacts with CO 2 to form SrCO 3 and can be regenerated by calcination. In the presence of moisture, SrO forms strontium hydroxide and its hydrates (Sr(OH) 2 ·nH 2 O). Here, this study, which employs density functional theory, investigates the CO 2 adsorption mechanism of these processes on various crystal surfaces, including SrO, Sr(OH) 2 , Sr(OH) 2 ·1H 2 O, and Sr(OH) 2 ·8H 2 O. A significant finding is that the interaction of CO 2 with these surfaces leads to carbonate/bicarbonate formation via electron transfer, with notable differences in CO 2 orientation and bond characteristics between SrO surfaces and its hydroxylated surfaces. To explore the effects of moisture on CO 2 adsorption, H 2 O adsorption on these stable surfaces was investigated. The results showed that H 2 O reacts with the SrO (100) surface to form hydroxyl (OH) groups while it bonds with the surfaces of Sr(OH) 2 ·nH 2 O (n = 0, 1, 8) with hydrogen bonding. A small amount of H 2 O can enhance CO2 adsorption while a large amount of H 2 O could decrease the capability of CO 2 adsorption.
High-throughput functional variant screens via in vivo production of single-stranded DNA
Significance We report a methodology for the pooled construction of mutants bearing precise genomic sequence variations and multiplex phenotypic characterization of these mutants using next-generation sequencing (NGS). Unlike existing techniques depending on CRISPR-Cas–directed genomic breaks for genome editing, this strategy instead uses single-stranded DNA produced by a retron element for recombineering. This enables libraries of millions of elements to be constructed and offers relaxed design constraints which permit natural DNA or random variation to be used as inputs.
Photosynthetic reaction center variants made via genetic code expansion show Tyr at M210 tunes the initial electron transfer mechanism
Significance Reaction centers (RCs) are critical to photosynthetic energy conversion. RCs in all characterized photosynthetic organisms contain two symmetrically arranged branches of chromophores and enable light-induced electron transfer with high yield. We fine-tune the properties of a key bacterial RC symmetry-breaking tyrosine via its replacement with noncanonical tyrosine analogs and determine kinetic outcomes. Results are interpreted through energetic characterization made possible by resonance Stark spectroscopy. Analysis indicates this tyrosine modulates the mechanism of the initial light-induced electron transfer, affording an alternative functional pathway that maintains the RC’s robust electron transfer. Modern molecular biology, ultrafast spectroscopy, crystallography, and energetic characterization enable the mechanistic model we describe. Our results deepen understanding of RC function and may have implications for other photocatalysts and enzymes.
Potent monoclonal antibody?mediated neutralization of a divergent Hendra virus variant
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Divergent evolution of extreme production of variant plant monounsaturated fatty acids
Metabolic extremes provide opportunities to understand enzymatic and metabolic plasticity and biotechnological tools for novel biomaterial production. We discovered that seed oils of many Thunbergia species contain up to 92% of the unusual monounsaturated petroselinic acid (18:1Δ6), one of the highest reported levels for a single fatty acid in plants. Supporting the biosynthetic origin of petroselinic acid, we identified a Δ6-stearoyl-acyl carrier protein (18:0-ACP) desaturase from Thunbergia laurifolia , closely related to a previously identified Δ6-palmitoyl-ACP desaturase that produces sapienic acid (16:1Δ6)-rich oils in Thunbergia alata seeds. Guided by a T. laurifolia desaturase crystal structure obtained in this study, enzyme mutagenesis identified key amino acids for functional divergence of Δ6 desaturases from the archetypal Δ9-18:0-ACP desaturase and mutations that result in nonnative enzyme regiospecificity. Furthermore, we demonstrate the utility of the T. laurifolia desaturase for the production of unusual monounsaturated fatty acids in engineered plant and bacterial hosts. Through stepwise metabolic engineering, we provide evidence that divergent evolution of extreme petroselinic acid and sapienic acid production arises from biosynthetic and metabolic functional specialization and enhanced expression of specific enzymes to accommodate metabolism of atypical substrates.
Factors underlying a latitudinal gradient in the S/G lignin monomer ratio in natural poplar variants
The chemical composition of wood plays a pivotal role in the adaptability and structural integrity of trees. However, few studies have investigated the environmental factors that determine lignin composition and its biological significance in plants. Here, we examined the lignin syringyl-to-guaiacyl (S/G) ratio in members of a Populus trichocarpa population sourced from their native habitat and conducted a genome wide association study to identify genes linked to lignin formation. Our results revealed many significant associations, suggesting that lignin biosynthesis is a complex polygenic trait. Additionally, we found an increase in the S/G ratio from northern to southern geographic origin of the trees sampled, along with a corresponding metabolic and transcriptional reprogramming of xylem cell wall biosynthesis. Further molecular analysis identified a mutation in a cell wall laccase genetically associated with higher S/G ratios that predominate in trees from warmer lower latitudes. Collectively, our findings suggest that lignin heterogeneity arises from an evolutionary process enabling poplar adaptation to different climatic challenges.