Studies of unusual catalysis : a tale of four enzymes from diverse biosynthesis pathways

The diverse reactions that enzymes catalyze have fascinated enzymologists for decades. Continuing investigations in the biosynthesis of both primary and secondary metabolites have led to the discovery of enzymes that employ unusual ways to mediate bio-transformations. Exploration of such atypical biological catalysts is not only important for a comprehensive understanding of the natural products biosynthesis, but also providing new insights that are potentially valuable for developing novel compounds with enhanced biological activities. This dissertation describes the characterization of four enzymes that demonstrate unusual catalytic properties in different biosynthesis pathways. UDP-galactopyranose mutase (UGM) is required for cell wall biosynthesis in many microorganisms. It uses the common cofactor flavin adenine dinucleotide (FAD) in an unusual manner. Positional isotope exchange and kinetic linear free energy relationship studies provide a direct experimental evaluation of the nucleophilic participation by reduced FAD during UGM catalysis. MoeZ from Amycolatopsis orientalis is a unique sulfur carrier protein (SCP) activating enzyme that participates in the metabolism of sulfur. Unlike reported pathway specific homologues, MoeZ can activate multiple SCPs from different biosynthesis pathways found in A. orientalis. Herein, the enzyme is characterized biochemically, and a disulfide intermediate is suggested as part of its catalytic cycle for sulfur transfer from thiosulfate to SCPs. The last two enzymes, Fom3 and OxsB, belong to the cobalamin-dependent radical SAM class of enzymes. While these enzymes are believed to operate with unprecedented chemistry, they remain poorly understood and understudied. Fom3 is proposed to methylate an unactivated carbon center in the biosynthesis of fosfomycin, which is a clinically relevant antibiotic. OxsB is responsible for the biosynthesis of oxetanocin A, an oxetane ring containing nucleoside that exhibits antiviral activity. Efforts have been made to isolate active Fom3 and reconstitute the in vitro activity of OxsB. Reductive cleavage of SAM by the latter enzyme has been demonstrated for the first time and is described in this dissertation.Pharmac

Spatial imaging of Zn and other elements in Huanglongbing-affected grapefruit by synchrotron-based micro X-ray fluorescence investigation

Huanglongbing (HLB) is a highly destructive, fast-spreading disease of citrus, causing substantial economic losses to the citrus industry worldwide. Nutrient levels and their cellular distribution patterns in stems and leaves of grapefruit were analysed after graft-inoculation with lemon scions containing 'Candidatus Liberibacter asiaticus' (Las), the heat-tolerant Asian type of the HLB bacterium. After 12 months, affected plants showed typical HLB symptoms and significantly reduced Zn concentrations in leaves. Micro-XRF imaging of Zn and other nutrients showed that preferential localization of Zn to phloem tissues was observed in the stems and leaves collected from healthy grapefruit plants, but was absent from HLB-affected samples. Quantitative analysis by using standard references revealed that Zn concentration in the phloem of veins in healthy leaves was more than 10 times higher than that in HLB-affected leaves. No significant variation was observed in the distribution patterns of other elements such as Ca in stems and leaves of grapefruit plants with or without graft-inoculation of infected lemon scions. These results suggest that reduced phloem transport of Zn is an important factor contributing to HLB-induced Zn deficiency in grapefruit. Our report provides the first in situ, cellular level visualization of elemental variations within the tissues of HLB-affected citrus. © 2014 © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology

The Face Semigroup Algebra of a Hyperplane Arrangement

This article presents a study of an algebra spanned by the faces of a hyperplane arrangement. The quiver with relations of the algebra is computed and the algebra is shown to be a Koszul algebra. It is shown that the algebra depends only on the intersection lattice of the hyperplane arrangement. A complete system of primitive orthogonal idempotents for the algebra is constructed and other algebraic structure is determined including: a description of the projective indecomposable modules; the Cartan invariants; projective resolutions of the simple modules; the Hochschild homology and cohomology; and the Koszul dual algebra. A new cohomology construction on posets is introduced and it is shown that the face semigroup algebra is isomorphic to the cohomology algebra when this construction is applied to the intersection lattice of the hyperplane arrangement.Comment: 37 pages, LaTeX; Added section 8.3B; Changed the wording of a few paragraphs in the introduction and abstract. No major change

Orthonectids Are Highly Degenerate Annelid Worms

The animal groups of Orthonectida and Dicyemida are tiny, extremely simple, vermiform endoparasites of various marine animals and have been linked in the Mesozoa (Figure 1). The Orthonectida (Figures 1A and 1B) have a few hundred cells, including a nervous system of just ten cells, and the Dicyemida (Figure 1C) are even simpler, with ∼40 cells. They are classic “Problematica”—the name Mesozoa suggests an evolutionary position intermediate between Protozoa and Metazoa (animals) and implies that their simplicity is a primitive state, but molecular data have shown they are members of Lophotrochozoa within Bilateria, which means that they derive from a more complex ancestor. Their precise affinities remain uncertain, however, and it is disputed whether they even constitute a clade. Ascertaining their affinities is complicated by the very fast evolution observed in their genes, potentially leading to the common systematic error of long-branch attraction (LBA). Here, we use mitochondrial and nuclear gene sequence data and show that both dicyemids and orthonectids are members of the Lophotrochozoa. Carefully addressing the effects of unequal rates of evolution, we show that the Mesozoa is polyphyletic. While the precise position of dicyemids remains unresolved within Lophotrochozoa, we identify orthonectids as members of the phylum Annelida. This result reveals one of the most extreme cases of body-plan simplification in the animal kingdom; our finding makes sense of an annelid-like cuticle in orthonectids and suggests that the circular muscle cells repeated along their body may be segmental in origin

Arsonium ylides in organic synthesis

postprin

Polystyrene-supported triphenylarsines: Useful ligands in palladium-catalyzed aryl halide homocoupling reactions and a catalyst for alkene epoxidation using hydrogen peroxide

The utility of both soluble (non-cross-linked) and insoluble (cross-linked) polystyrene-supported triphenylarsine reagents were examined. These reagents were prepared by standard radical polymerization methodology and used in palladium-catalyzed homocoupling reactions of aryl halides. The insoluble reagent was also used as a catalyst precursor in heterogeneous alkene epoxidation reactions in which aqueous hydrogen peroxide was the stoichiometric oxidant. For the aryl halide homocoupling reactions, both reagents worked well and afforded similar results. Unhindered aryl iodides afforded the best yields in the shortest reaction times compared to aryl bromides. The epoxidation reactions of unfunctionalized alkenes were not very efficient. This was probably due to the hydrophobicity of the polystyrene matrix, which did not swell in the reaction medium. Thus, since a microporous, gel-type polystyrene matrix was used, the majority of the arsine groups were inaccessible to the reaction components and therefore incapable of participating in catalysis. © 2005 Elsevier Ltd. All rights reserved.postprin

The mitochondrial genomes of the acoelomorph worms Paratomella rubra, Isodiametra pulchra and Archaphanostoma ylvae

Acoels are small, ubiquitous - but understudied - marine worms with a very simple body plan. Their internal phylogeny is still not fully resolved, and the position of their proposed phylum Xenacoelomorpha remains debated. Here we describe mitochondrial genome sequences from the acoels Paratomella rubra and Isodiametra pulchra, and the complete mitochondrial genome of the acoel Archaphanostoma ylvae. The P. rubra and A. ylvae sequences are typical for metazoans in size and gene content. The larger I. pulchra  mitochondrial genome contains both ribosomal genes, 21 tRNAs, but only 11 protein-coding genes. We find evidence suggesting a duplicated sequence in the I. pulchra mitochondrial genome. The P. rubra, I. pulchra and A. ylvae mitochondria have a unique genome organisation in comparison to other metazoan mitochondrial genomes. We found a large degree of protein-coding gene and tRNA overlap with little non-coding sequence in the compact P. rubra genome. Conversely, the A. ylvae and I. pulchra genomes have many long non-coding sequences between genes, likely driving genome size expansion in the latter. Phylogenetic trees inferred from mitochondrial genes retrieve Xenacoelomorpha as an early branching taxon in the deuterostomes. Sequence divergence analysis between P. rubra sampled in England and Spain indicates cryptic diversity

Coherent phonon dynamics in semiconductors

Ultrafast pump-probe spectroscopy is a powerful experimental technique to study the light-matter interaction and ultrafast dynamics in solids. In many semiconductors, under ultrafast laser irradiation, phonons (quantized lattice vibrations) with both temporal and spatial coherence can be generated conveniently. When a stronger laser pulse excites coherent phonons that induce refractive index change, and thus the reflectivity change of the materials, the time-dependent phonon dynamics can be detected by a delayed probe pulse. The generation and detection of coherent phonons provide an opportunity to understand the fundamental physics between light and matter interaction, as well as a path to manipulate other physical processes, for applications such as sound amplification stimulated emission (SASER), phonon mode manipulation, ultrafast phase switching, superconductivity enhancement and manipulation of magnetism¹⁻⁵. This thesis presents a series of time-resolved studies of coherent phonons in three semiconductor systems, including bulk CdSe, Bi₂Te₃/Sb₂Te₃ superlattice and GaAs/AlAs superlattice. In bulk CdSe, a material extensively studied for quantum dot photoelectronics, coherent phonons serve as the probe for the reversible ultrafast melting. In Bi₂Te₃/Sb₂Te₃ superlattice, a material system used for thermoelectrics, the coherent thermal phonons are excited directly and are found to be selectively filtered in the superlattice structure compared with bulk materials. In GaAs/AlAs superlattice, a quantum well structure for photodetectors and lasers, a strong quantum coherent coupling among different phonon modes is observed. A similar coherent coupling between photons and phonons has been used to induce and enhance superconductivity [superscript 6,7] and mimic the magnetic field⁸. However, direct observation of nonlinear phonon coupling is rare. Moreover, a novel technique based on surface plasmon resonance has been implemented into the pump-probe spectrometer to improve detection efficiencyMaterials Science and Engineerin

Fundamental Aspects of the ISM Fractality

The ubiquitous clumpy state of the ISM raises a fundamental and open problem of physics, which is the correct statistical treatment of systems dominated by long range interactions. A simple solvable hierarchical model is presented which explains why systems dominated by gravity prefer to adopt a fractal dimension around 2 or less, like the cold ISM and large scale structures. This has direct relation with the general transparency, or blackness, of the Universe.Comment: 6 pages, LaTeX2e, crckapb macro, no figure, uuencoded compressed tar file. To be published in the proceeedings of the "Dust-Morphology" conference, Johannesburg, 22-26 January, 1996, D. Block (ed.), (Kluwer Dordrecht