An intriguing mystery about tryptophan 2, 3-dioxygenase is its hydrogen peroxide-triggered enzyme reactivation from the resting ferric oxidation state to the catalytically active ferrous form. In this study, we found that such an odd Fe(III) reduction by an oxidant depends on the presence of L-Trp, which ultimately serves as the reductant for the enzyme. In the peroxide reaction with tryptophan 2, 3-dioxygenase, a previously unknown catalase-like activity was detected. A ferryl species (δ = 0.055 mm/s and ΔEQ = 1.755 mm/s) and a protein-based free radical (g = 2.0028 and 1.72 millitesla linewidth) were characterized by Mössbauer and EPR spectroscopy, respectively. This is the first compound ES-type of ferryl intermediate from a heme-based dioxygenase characterized by EPR and Mössbauer spectroscopy. Density functional theory calculations revealed the contribution of secondary ligand sphere to the spectroscopic properties of the ferryl species. A Trp-Trp dimer and a monooxygenated L-Trp were both observed as the enzyme reactivation by-products by mass spectrometry. Together, these results lead to the unraveling of an over 60-year old mystery of peroxide reactivation mechanism.

Natural nitro compounds with diverse structures and biological functions are produced by bacteria, fungi, plants and animals. Little is known about the behavior of such compounds in natural ecosystems. The lack of accumulation in the biosphere implies that they are biodegraded. Microbial strategies for biodegradation of synthetic nitro compounds are well established; however only two pathways are known for degradation of natural nitro compounds. The research described here examines the genes that encode the key enzymes required for biodegradation of 3-nitrotyrosine (3NTyr) and 1-nitro-2-phenylethane (NPE). 3NTyr is a biological marker for disease and inflammation in plants and animals. A 3NTyr degrading microbe, Variovorax sp. JS669 was isolated from soil. We identified the JS669 denA, which encodes an enzyme that catalyzes denitration of 4-hydroxy-3-nitro-phenylacetate, the key step in metabolism of 3NTyr. The isolation of 3NTyr degraders and development of molecular probes specific to denA revealed that 3NTyr degradation is a widespread phenomena in natural habitats and the compound is metabolized by phylogenetically diverse bacteria. Phylogenetic analysis of the 4-hydroxy-3-nitro-phenylacetate denitrase from JS669 revealed it to be the first functionally annotated protein in a clade of unidentified Class A flavin monooxygenases. NPE has been identified from several plants, yet the biodegradation of the compound remained a mystery. Here we report the degradation of NPE and its analog 2-nitropropylbenzene. Discovery of the metabolic pathway revealed a novel microbial strategy to use a meta-ring fission degradation pathway to cleave an undesirable side chain from an aromatic compound and use the remainder of the compound as a carbon and energy source. Two genes that encode enzymes in the biodegradation pathway were identified and both are deeply branched within their respective phylogenetic trees, indicating that both represent highly specialized microbial enzymes. Furthermore, microbial degradation of NPE resulted in the production of 3-nitropropionic acid, a natural toxin that inhibits succinate dehydrogenase and is responsible for livestock illness and death. This is the first report of bacterial production of 3-nitropropionic acid, and might represent a significant source of 3-nitropropionic acid in natural habitats. The findings from these studies contribute to the overall understanding of microbial metabolism. Specifically, this research reveals genes that encode novel enzymes and strategies for the biodegradation of two natural nitro compounds. Furthermore, discovery of mechanisms for the biodegradation of such compounds reveals novel microbial metabolic diversity and provides insight into the evolution of degradation pathways for synthetic compounds.

Inorganic phosphate (Pi) plays a critical role in many biological structures and processes. However, Pi typically occurs at low concentrations, particularly in marine environments. In comparison, naturally occurring organophosphonates, which are characterized by a stable carbon-phosphorus (CP) bond, are frequently present at higher concentrations. Accordingly, bacteria have evolved different mechanisms for cleaving the CP bond of organophosphonates to liberate Pi for metabolic use. Two prominent enzyme pathways for catabolic cleavage of a CP bond are examined in this thesis. The first, called CP-lyase, is encoded by the phn operon that consists of 14 genes (phnCDEFGHIJKLMNOP). CP-lyase has long been of interest for its ability to degrade a wide array of organophosphonates through a homolytic CP bond cleaving reaction. A soluble protein complex consisting of PhnGHIJK was isolated from E. coli, suggesting that protein-protein interactions are important for CP bond cleavage. Intermediates of organophosphonate catabolism by E. coli CP-lyase were also detected and isolated, including -D-ribosyl-1,2-cyclic phosphate and N-acetylated aminoalkylphosphonates, 2-N-acetamidoethylphosphonate and 5’-phospho--D-ribosyl-1’-alkylphosphonates. The former compound was shown to be converted by the phosphodiesterase PhnP to -D-ribosyl-1-phosphate. It was also shown that PhnO is an aminoalkylphosphonate N-acetyl transferase and that N-acetylation by this enzyme is necessary for CP bond cleavage of 1-aminoalklyphosphonates. These results demonstrated that in addition to forming protein complexes, CP-lyase also comprises a catabolic pathway, with ribosylation of organophosphonates playing a key part in setting up the CP bond cleaving reaction. The second pathway examined in this thesis is comprised of marine bacterial enzymes PhnY and PhnZ and is specific for 2-aminoethylphosphonate. PhnY was shown to be an -ketoglutarate / Fe(II) dependent dioxygenase that hydroxylates the -carbon of 2-aminoethylphosphonate to form (R)-2-amino-1-hydroxyethylphosphonate. PhnZ was shown to be a novel Fe(II) dependent oxygenase that converts (R)-2-amino-1-hydroxyethylphosphonate to glycine and Pi. Site directed mutagenesis, kinetic analysis, reactions with substrate analogues, and X-ray crystallography examined the roles of active site residues and the di-iron active site. Additionally, a unique induced-fit mechanism was discovered which appears to synchronize substrate binding with activation of molecular oxygen. Overall these results show that PhnZ represents a new mechanism for catabolic cleavage of a CP bond. / Thesis (Ph.D, Chemistry) -- Queen's University, 2013-09-13 16:24:17.261

No description available.

This thesis describes a molecular-based study undertaken to analyse the expression of the RAMOSUS1 (RMS1) and RAMOSUS5 (RMS5) genes in pea (Pisum sativum). Both genes encode carotenoid cleavage dioxygenase (CCD) enzymes that are together proposed to control the synthesis of an inhibitor of bud outgrowth termed SMS (Shoot Multiplication Signal). SMS was recently identified as strigolactone. Expression analyses of RMS1 presented here have built upon earlier experiments which demonstrate it to be a highly regulated transcript. RMS1 mRNA levels are known to be rapidly decreased following removal of the shoot apex but are subsequently restored to that of intact plants by auxin (indole-3-acetic acid or IAA). This regulatory mechanism is retained in all five ramosus mutants tested to date. Together with physiological data, this indicates RMS1, and therefore SMS, are required in IAA-mediated suppression of bud outgrowth. Another significant aspect of RMS1 regulation identified in previous studies involves a graft-transmissible, long-distance feedback signal that moves from shoot to root. This feedback regulation is dependent on the RMS2 gene and enhances RMS1 expression levels. Prior to the cloning of RMS5 and its discovery as a second CCD enzyme in the RMS network, reciprocal grafting studies with the rms mutants indicated RMS5 may act in the same pathway as RMS1 to produce SMS. Multiple studies presented here demonstrate that these two CCD genes are expressed in similar tissues and are regulated by the same signals, specifically IAA and the RMS2-dependent feedback signal. Like RMS1, the RMS5 gene also retains its IAA response in the rms mutants. However, RMS5 is generally less responsive to changes in IAA and RMS2-dependent feedback, as it exhibits smaller fluctuations than RMS1 in its expression levels. Together these findings support a general view that RMS1 is more likely to control a rate-limiting step in SMS synthesis. A previous study indicated that RMS1 expression may be up-regulated by IAA through a posttranscriptional mechanism. This thesis sought to more closely examine the RMS1 and RMS5 IAA response by separately observing the effect of IAA on subsequent transcription. New transcripts, termed heterogenous nuclear RNAs (hnRNAs), were relatively quantified in parallel with existing mRNAs in the steady-state cytoplasmic pool. The experiments conducted here provide further evidence that IAA may act post-transcriptionally to stabilise RMS1 mRNA because the changes in hnRNA are not proportional to the changes in mRNA following IAA-modifying treatments. IAA may still function to induce transcription of RMS1, but this does not appear to be a significant mechanism by which IAA regulates RMS1 expression. In contrast, the IAA induction of RMS5 occurs predominantly via new transcription and RMS5 either lacks or is not as strongly subjected to the IAA-mediated mRNA stabilisation mechanism proposed for RMS1. Initial studies described in this thesis also suggest that IAA could act to regulate the expression of the Arabidopsis orthologues MORE AXILLARY BRANCHING (MAX) genes via a post-transcriptional mechanism. Analyses of MAX hnRNA and mRNA levels in Arabidopsis to date indicate it is the RMS5 orthologue MAX3 which exhibits an IAA response most like RMS1. Additional studies into the regulation of RMS1 and RMS5 presented in this thesis provide further insights into the molecular mechanisms controlling their expression levels. In vitro experiments with the translation inhibitor cycloheximide demonstrate that RMS5 expression levels are increased when protein synthesis is reduced, as previously shown for RMS1. Relative quantification of RMS1 and RMS5 hnRNA levels further demonstrate that the induction by cycloheximide is due primarily to an increase in new transcription, indicating that RMS1 and RMS5 are negatively regulated by a rapidly turned-over transcriptional repressor. Tissue specific effects on RMS1 expression were also observed which are consistent with a protein degradation function of the RMS4 F-box in the shoot. This thesis provides further evidence to suggest that SMS acts in concert with IAA to inhibit the sustained outgrowth of axillary buds. RMS1 and RMS5 expression levels are not regulated by a hypothetical fast decapitation signal which is proposed to cause the initial bud outgrowth occurring prior to decapitation-induced IAA depletion. RMS1, RMS5 and SMS are therefore unlikely to control the initial exit of buds from dormancy to an intermediate transition state. Studies here also suggest that enhanced shoot auxin transport and cytokinin biosynthesis are associated with axillary bud outgrowth because the rms mutants contain elevated shoot expression levels of a gene encoding the auxin efflux carrier PIN1 and two genes controlling cytokinin biosynthesis. Several approaches described in this study were used to characterise the RMS1 and RMS5 proteins. Anti-peptide antibodies were generated against both proteins and the results obtained show that although the antibodies are likely to recognise the full-length proteins, further work is required to effectively detect RMS1 and RMS5 in plant tissues via western blotting. Preliminary in situ immunolocalisation results indicate the RMS1 and RMS5 proteins are localised to the vasculature, consistent with gene expression analyses.

No description available.

Metal ions are ubiquitously found in all living systems and play vital roles in supporting life forms by performing an array of biological activities. Such biological activities include binding and transforming organic molecules, and also acting as active centers and cofactors for catalysis of various acid-base and redox reactions in biological system. The main focus in bioinorganic chemistry is to elucidate the structural and functional roles of metals in biological systems. Among all transition metal ions, Cu2+ and Fe3+ are especially versatile and important due to their abilities to go through redox efficiently. This dissertation can be divided into four main chapters. The bioinorganic chemistry of Cu- and Fe-containing proteins were briefly discussed in Chapter one. The next chapter focuses on bacitracin, a cyclic peptide-based antibiotic produced by soil bacteria Bacillus subtilis. Bacitracin is a metalloantibiotics that can coordinate with many transition metal ions and exhibit different biological activities. In the first part of Chapter two, the aim is to explore the chemicals interactions in soil micro-ecology by investigating the interactions of different flavonoids and Cu(II)-bacitracin complex. The second part of chapter two demonstrated the binding and oxidation activity of iron(III)-bacitracin. Metal-mediated oxidative stress plays a crucial role in the development of different neurodegenerative diseases. In chapter 3, various synthetic and natural compounds were used to inhibit the oxidation chemistry mediated by Cu(II)-beta-amyloid complex associated with Alzheimer’s disease. Many proteins incorporate copper ions at their active sites for different functions, and among all of the chemistry copper-containing-proteins can perform, one of the most interesting aspect is the ability to bind and activate O2. Therefore, the biomimetic of two different Cu(II) complexes were investigated. In all studies, a combination of kinetic and different spectroscopic methods (UV-vis, NMR and resonance Raman spectroscopy) were used to study their metal binding and activity.

Die Toluol-Dioxygenase von Pseudomonas putida F1 ist eine Rieske-Dioxygenase und besteht aus Reduktase-, Ferredoxin- und Oxygenase-Komponente. Sie katalysiert den ersten Schritt im aeroben Abbau von Toluol. Ein effizienter Elektronentransfer zur terminalen Oxygenase-Komponente - an der die Sauerstoffaktivierung und Umwandlung von Toluol zum cis-Toluol-Dihydrodiol stattfindet - setzt eine reibungslose Interaktion aller Komponenten voraus. Die Ergebnisse der Stopped-flow-Messungen in der reduktiven Halbreaktion zeigen, dass NADH die Reduktase mittels Hydridtransfer reduziert, wodurch ein stabiler Ladungstransfer-Komplex zwischen NAD+ und FADH- entsteht. In der oxidativen Halbreaktion wird dieser dann durch einen Elektronenakzeptor über das blaue Semichinon zum Chinon oxidiert. Dabei zeigt sich, dass der Ladungstransfer-Komplex die Reaktion der Reduktase mit Sauerstoff unterdrückt. Eine Erklärung hierfür liefert die Kristallstruktur des Ladungstransfer-Komplexes. Die Reaktion mit Sauerstoff wird dadurch unterdrückt, dass das NAD+ koplanar mit dem Isoalloxazinring ist und den reaktiven N5-C4a Teil des FADs schützt und zudem den Isoalloxazinring in eine planare, weniger sauerstoffempfindliche Konformation zwängt. Durch die Bildung des Reduktase-Ferredoxin-Komplexes wird ein effizienter Elektronentransfer folgendermaßen ermöglicht: a) das Ferredoxin bindet an die Reduktase aufgrund elektrostatischer Anziehung entgegengesetzter Oberflächenladungen beider Proteine, b) die hydrophobe Region, die die beiden Redoxzentren umgibt, fungiert als Ein- und Ausgang für Elektronen und c) die geringe Entfernung von 11.7 Å zwischen beiden Kofaktoren erlaubt einen schnellen Elektronentransfer. Die Ergebnisse dieser Arbeit zeigen, dass der Elektronentransfer zwischen Reduktase und Ferredoxin durch die Bildung eines stabilen Ladungstransfer- und Reduktase- Ferredoxin-Komplexes beeinflusst wird und dadurch das Problem einer ungewollten Reaktion mit Sauerstoff umgangen wird. / The toluene dioxygenase from Pseudomonas putida F1 is a three-component Rieske non-heme iron dioxygenase comprising of a reductase, ferredoxin and an oxygenase component. It catalyzes the initial step in the aerobic degradation of toluene to cis-toluene dihydrodiol. A smooth interaction between all three components needs to be ensured to efficiently transfer the electrons derived from NADH oxidation to the terminal oxygenase component where molecular oxygen is activated and used for the hydroxylation of toluene. The results of the kinetic studies of the reductive half reaction of reductase reveal that NADH reduces the reductase, resulting in the formation of a stable charge transfer complex between NAD+ and FADH-. Oxidation of the charge transfer complex by an electron acceptor proceeds via the neutral semiquinone to the quinone state of FAD. It is shown that the charge transfer complex suppresses the reaction of the reductase with dioxygen. An explanation for this change in reactivity can be deduced from the structure of the charge transfer complex. Its slower reaction with dioxygen results from NAD+ lying coplanar with the FAD shielding its reactive N5-C4a locus and the forced planarity of the isoalloxazine ring. The formation of the reductase-ferredoxin complex allows efficient electron transfer from reductase to ferredoxin because a) the oppositely charged interacting surfaces of both proteins facilitate the pre-orientation of the ferredoxin on the reductase, b) a hydrophobic region surrounding the two redox centers in the complex acts as an exit/entrance port for electrons and c) the short edge-to-edge distance between both cofactors of 11.7 Å guarantees a fast electron transfer. The results demonstrate that the electron transfer between reductase and ferredoxin is governed by the formation of a stable charge transfer and of a reductase-ferredoxin complex with which the problem of an unwanted side reaction with dioxygen is obviated.

Submitted by orjuela@ibilce.unesp.br (orjuela@ibilce.unesp.br) on 2016-02-17T12:16:38Z No. of bitstreams: 1 Isolamento de bactérias degradadoras de hidrocarbonetos aromáticos 1-107.pdf: 3940758 bytes, checksum: c39dfe1dada0d918848470d3f0de5b83 (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-02-17T13:16:08Z (GMT) No. of bitstreams: 1 orjuela_gl_dr_rcla.pdf: 3940758 bytes, checksum: c39dfe1dada0d918848470d3f0de5b83 (MD5) / Made available in DSpace on 2016-02-17T13:16:08Z (GMT). No. of bitstreams: 1 orjuela_gl_dr_rcla.pdf: 3940758 bytes, checksum: c39dfe1dada0d918848470d3f0de5b83 (MD5) Previous issue date: 2016-02-11 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Este documento foi organizado em dois capítulos. O Capítulo I é um artigo de revisão intitulado “Metabolic Pathways for Aromatic Compounds Degradation by Bacteria”, no qual são descritas as fontes naturais e antrópicas dos hidrocarbonetos aromáticos e suas características químicas. Relacionaram-se os fatores ambientais que afetam a degradação aeróbia e anaeróbia desses compostos por bactérias e os principais compostos intermediários produzidos. É descrita passo a passo a sequência de preparação e desaromatização do anel benzênico e os compostos finais dessa degradação. O artigo foi publicado no volume 237 da série Reviews of Environmental Contamination and Toxicology em janeiro de 2016 (Springer http://dx.doi.org/10.1007/978-3-319-23573-8_5). O Capítulo II contém os resultados da pesquisa desenvolvida. O objetivo geral foi isolar cepas bacterianas de amostras de solo e avaliar o potencial degradador de fenol e outros hidrocarbonetos aromáticos. Foram realizadas coletas de amostras de solo de cinco postos de combustíveis, para a seleção das cepas bacterianas e para análises químicas e granulométricas. Alíquotas das amostras de solo foram transferidas para meio de cultura seletivo contendo querosene como única fonte de carbono. Testes morfológicos e bioquímicos indicaram que as cepas isoladas são Gram negativas, móveis, catalase positivas, produtoras de cápsula e de biossurfactantes. O sequenciamento do gene 16S rRNA mostrou 99 a 100% de similaridade com o gênero Pseudomonas sp. Todas as cepas degradaram o fenol em concentração de 120 mg L-1 em menos de 24 horas. Testes da atividade enzimática mostraram que algumas das cepas expressaram a catecol 1,2-dioxigenase que catalisa a orto-clivagem do anel benzênico e outras expressaram a catecol 2,3 dioxigenase da meta-clivagem do anel aromático. Uma cepa não apresentou atividade para nenhuma dessas duas enzimas e uma apresentou atividade de ambas. Todas as cepas foram capazes de crescer em presença de fenantreno, fluoranteno e pireno. / This document is organized in two chapters. The Chapter I is a review paper entitled “Metabolic Pathways for Aromatic Compounds Degradation by Bacteria” in which are described natural and anthropogenic sources of aromatic hydrocarbons and their chemical characteristics. There are listed environmental factors that affect the aerobic and anaerobic degradation by bacteria and the central intermediates yielded. It is described step to step of sequence of preparation and dearomatization of benzene ring and the final metabolites of breakdown. The manuscript was publicated in the volume 237 of Reviews of Environmental Contamination and Toxicology in January of 2016 (Springer http://dx.doi.org/10.1007/978-3- 319-23573-8_5). Chapter II has the results of developed research. The general objective was to isolate bacterial strains from samples of soil and to evaluate the potential of them for breakdown hydrocarbons. Soil samples from five gas stations were collected to isolate the bacterial strains and chemical and granulometric analysis was made. Aliquots of the soil samples were cultured with selective media with kerosene as only carbon and energy sources. Morphological and biochemical tests showed that bacterial strains were Gram negatives, motile, positive catalase, capsule-producers and biosurfactant producers. The sequencing of 16S rRNA gene showed 99 to 100% similarity with Pseudomonas sp genera. All bacterial strains were able to degrade phenol 120 mg L-1 in less than 24 hours. Tests of enzymatic activity showed that some bacteria expressed the catecol 1,2-dioxygenase that catalyze ortoclivage of benzene ring, others showed activity for the catecol 2,3-dioxygenase that catalyze the meta-cleavage of the ring. One strain did not show activity for any of these enzymes and one strain had activity for both. All strains were able to growth with fenantrene, fluoranthene and pyrene. / CNPq: 140704/2012-4

No description available.