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Nonheme iron(II) oxygenases within a common 2-His-1-carboxylate binding motif catalyze a wide range of oxidation reactions involved in biological functions like DNA repair and secondary metabolic processes. The mechanism of O2 activation catalyzed by this enzyme family has been examined by spectroscopic, crystallographic, and computational studies, where it is clear the iron(II) center works with substrate, and cosubstrate to activate O2 by forming a highly oxidizing iron species (iron(IV)-oxo). From a thermodynamic perspective, substrate and/or co-substrate binding organizes the active site for O2 activation, and understanding the interactions among metal, substrate, cosubstrate, and enzyme provides insight into the intramolecular contacts that guide the reaction catalyzed by the enzymes. This dissertation is focused on elucidating the interactions between metal, substrate, and co-substrate in a representative enzyme subfamily of nonheme iron(II) oxygenases, namely the 2-oxoglutarate dependent dioxygenases. Specifically, we investigated the thermodynamic properties of divalent metal ions binding to taurine-dependent dioxygenase (TauD), using Mn2+, Fe2+, and Co2+ ions. Additionally, the thermodynamics associated with substrate and co-substrate binding to Fe·TauD and iron(II)-ethylene forming enzyme (Fe·EFE) were explored using calorimetry and other biophysical techniques.

Les métabolismes du carbone et de l’azote sont étroitement coordonnés chez tous les organismes vivants en raison de l’importance de ces deux éléments dans les différents mécanismes physiologiques. Le 2-oxoglutarate (2-OG) est une molécule signal conservée chez tous les organismes et est impliqué dans la balance carbone / azote. Malgré son importance, il n’existe pas d’outil permettant de mesurer la concentration de 2-OG à l’échelle cellulaire. Pour combler cette carence, nous avons utilisé Anabaena sp. PCC 7120 pour construire un système de quantification du 2-OG in vitro et in vivo. Cette bactérie appartient au groupe des cyanobactéries qui contribuent aussi bien au cycle du carbone via la photosynthèse qu’au cycle de l’azote via leur métabolisme.Au cours de ma thèse, j’ai construit différents types de biosenseurs au 2-OG en utilisant les techniques de FRET (Fluorescence Resonance Energy Transfer). Ces biosenseurs sont capables de mesurer le 2-OG in vitro et permettent de le détecter in vivo en utilisant l’analyse à l’échelle de la cellule unique et la microscopie en temps réel. Nous avons découvert l’existence de variations dynamiques du 2-OG au niveau des filaments et le profil formé semble correspondre au futur profil de développent cellulaire. En raison de la conservation du rôle régulateur du 2-OG dans de nombreuses activités cellulaires, le biosenseur développé durant ma thèse pourrait être appliqué à une grande variété d’organismes dont les bactéries, les plantes, les animaux et les humains. / Carbon and nitrogen metabolisms are tightly coordinated in all living organisms because of the importance of the two elements in the physiology. 2-oxoglutarate (2-OG) is a signal conserved in all living organisms involved in the balancing between carbon and nitrogen metabolisms; however, despite its importance, it is currently impossible to measure 2-OG in each cells under different conditions when 2-OG is subject to variations Cyanobacteria contribute to global carbon cycle by oxygenic photosynthesis as well as to global nitrogen cycle through their nitrogen metabolism and in this study, we used the cyanobacterium Anabaena PCC 7120 as a model, to construct a system for the quantification of 2-OG in vitro and in vivo.. During my thesis, I took the advantages of the FRET (Fluorescence Resonance Energy Transfer) techniques and constructed several 2-OG biosensors that can adequately detect 2-OG levels in vitro in a quantitative manner. I tested their performance for the detection of 2-OG in vivo by using single-cell analysis and time-lapse microscopy. We found that 2-OG display dynamic changes at single-cell basis, and these variations are strongly correlated to cell differentiation activities. The 2-OG biosensors developed during my thesis can be applied in a wide range of organisms, including other bacteria, plants, animals, and human, because of the conserved roles of 2-OG in regulating a variety of cellular activities.

The 2-oxoglutarate and ferrous ion dependent oxygenases are a super family of enzymes that are involved in a wide range of biological processes regulated trough the mechanism of post-translational modification (PTM). Such biological processes include hypoxia sensing (through regulating HIF transcription), fatty acid metabolism (through carnitine production), transcriptional regulation (through demethylation of histones), and collagen structure formation (through proline and lysine hydroxylation). To understand the underlying mechanisms of such regulatory processes, and to develop clinically useful inhibitors, and thereby regulate these processes in living organisms, requires sensitive methods for monitoring enzyme activity. The use of indirect methods such as quantification of reaction products (14CO2 or succinate) can be problematic, as both products can result from competitive reactions. Alternative direct measurement of substrate modifications using mass spectrometry-based proteomics can be applied; however, (1) for this technique the limit of detection is often prohibitive, (2) the method is best suited for the confirmation of known modifications, rather than for the discovery of new modifications, and (3) sequence coverage may often be only 60%, and therefore many modifications can be missed. The aim of the research presented in this thesis was to develop amino acid analysis and to apply these methods to the identification and quantification of PTMs catalysed by 2-oxoglutarate and ferrous ion dependent oxygenases. A range of LC-MS approaches were investigated including: (1) C18 reversed phase chromatography of quinoline derivatised amino acids, (2) ion paring chromatography, and (3) mixed mode chromatography with either UV, or conventional molecular MS, or isotope ratio mass spectrometry detection. Analysis of the elution patterns for those separation techniques enabled estimation of the retention parameters of modified amino acids and the identification of the modifications, where no standards were available. The most sensitive approach developed employed mixed mode chromatography coupled to isotope ratio mass spectrometry which was optimised for the analysis of modified amino acids. This was shown to have a limit of detection two orders of magnitude lower (0.01μM) than other conventional mass spectrometry techniques. Using amino acid labelling in cell culture, a quantification protocol was developed which employed a non-labelled internal standard and selectively labelled cell culture. The method was shown to be suitable for both very accurate quantification at low concentration levels and metabolic studies, allowing us to track back the modifications to their precursors. The analytical methods developed for amino acid analysis were successfully applied to the analysis of modifications resulting from 2-oxoglutarate and Fe dependent oxygenase activity. Stereochemistry of lysyl hydroxylation in the splicing regulatory protein Luk7L2 by JmjD6 as well as of the self hydroxylation of the JmjD6 was identified. The stereochemistry was shown to be different from that of previously reported for the collagen hydroxyline, hydroxylated by the another member of this enzyme family. mbP4H enzyme was shown to catalyse prolyl hydroxylation of taODD resulting in 4R-hydroxyprolyl. Amino acid analysis was used in order to verify the mechanism of the hBBOX catalysed rearrangement of Mildronate. Using the method developed for the analysis of non-derivatised amino acids the screening of potential substrates of hBBOX enzyme was carried out and two new substrates were identified. The isotope ratio mass spectrometry protocol was applied to the study of histones from cell culture; low levels of hydroxylated and methylated amino acids were quantified. The analytical methods described were developed to complement to the well established proteomics techniques. The methods developed enable investigation into the region- and stereo- chemistry of the modified groups within the modified AA residue and has proved to be a powerful tool of exploratory PTM analysis.

Abstract Lysyl hydroxylases (E.C. 1.14.11.4, LHs) have three isoenzymes that are found in humans and mice, and they hydroxylate lysine residues in collagens and other proteins containing collagenous sequences. The hydroxylysines formed are crucial for the intermolecular collagen crosslinks that stabilise collagen fibres, thereby providing the stiffness and stability required by various tissues. In addition, hydroxylysines serve as attachment sites for carbohydrates, whose functions on collagen molecules are not completely understood yet. In humans, lack of LH1 causes Ehlers-Danlos syndrome (EDS) VIA, which is characterised, for example, by severe progressive kyphoscoliosis and muscular hypotonia with joint laxity. Mutations in the LH2 gene are associated with Bruck syndrome, which is characterised by fragile bones with congenital joint contractures. In the present work recombinant human lysyl hydroxylases were produced in insect cells and purified to homogeneity. Limited proteolysis revealed that LHs consist of at least three structural domains. The N-terminal domain plays no role in the lysyl hydroxylase activity, but instead, is responsible for the recently reported glucosyltransferase activity of LH3, and the galactosyltransferase activity reported here for the first time. The LH polypeptide lacking the N-terminal domain is a fully active LH with Km values identical to those of full-length enzyme. In addition, direct evidence is shown that LH2, but not LH1 or LH3, hydroxylates the telopeptide lysine residues of fibrillar collagens. All three recombinant LHs were able to hydroxylate the synthetic peptides representing the helical hydroxylation sites in types I and IV collagens, with some differences in the Vmax and Km values. In addition, all three LHs hydroxylated the collagenous domain of coexpressed type I procollagen chain to similar extend. In this study mouse lines lacking LH3 or LH1 were created and analysed. Unexpectedly, the LH3 null mice died during the embryonal period due to fragmentation of basement membranes. Type IV collagen, one of the major components in basement membranes, aggregates on its way to extracellular space and is absent from the basement membranes making them fragile. This is most probably caused by abnormal processing of type IV collagen due to decreased glucosyltransferase activity of the LH3 null embryos. The first mouse model for human EDS VIA is presented here. The LH1 null mice did not have kyphoscoliosis characteristic of EDS VIA, but showed gait abnormalities due to muscular hypotonia and possible joint laxity, as also seen in EDS VIA patients. In addition, the null mice died occasionally from aortic ruptures. Ultra structural analysis revealed degradation of smooth muscle cells and abnormal collagen fibres even in non-ruptured aortas of LH1 null mice. The hydroxylation of lysine residues and crosslinking in LH1 null mice were also abnormal, as in human EDS VIA patients. The LH1 null mouse line provides an excellent tool for analysing several aspects of human EDS VIA, including muscular hypotonia, abnormalities in collagen fibres and their crosslinking.

Abstract Lysyl hydroxylase (EC 1.14.11.4, procollagen-lysine, 2-oxyglutarate, 5-dioxygenase, Plod) catalyzes the hydroxylation of certain lysine residues in collagens and in other proteins with collagenous domains. Three lysyl hydroxylase isoforms have been cloned from human and rat. The importance of lysyl hydroxylase 1 in collagen biosynthesis is demonstrated by the heritable disorder, Ehlers-Danlos syndrome type VI, which is characterized by joint laxity, progressive scoliosis, muscle hypotonia, scleral fragility and rupture of the ocular globe. An alternatively spliced form of lysyl hydroxylase 2 seems to function as a telopeptide lysyl hydroxylase. Lysyl hydroxylase 3 has three enzyme activities, lysyl hydroxylase, hydroxylysyl galactosyltransferase (EC 2.4.1.50), and galactosylhydroxylysyl glucosyltransferase (EC 2.4.1.66) activities that have been demonstrated earlier with in vitro experiments. In this thesis study, the cDNAs of mouse lysyl hydroxylase isoforms 1, 2 and 3 were cloned and characterized and the gene structures of lysyl hydroxylase 2, Plod2, and lysyl hydroxylase 3, Plod3, were determined. Mouse lysyl hydroxylase isoforms were found to be highly homologous to the corresponding human isoforms and they were approximately 60% identical with each other. The mouse Plod3 gene has 19 exons as do the human PLOD1 and PLOD3 genes, and mouse Plod2, like the human PLOD2, has 20 exons including one alternatively spliced extra exon. The mouse isoforms were also found to have distinct tissue distributions. Phylogenetic analysis revealed that the lysyl hydroxylase genes have evolved from an ancestral gene through two gene duplication events. Lysyl hydroxylase 3 was demonstrated to be the oldest isoform, which is further supported by the association of glycosyltransferase activities with lysyl hydroxylase 3 and with the only lysyl hydroxylase of Caenorhabditis elegans. The roles of the different enzyme activities of lysyl hydroxylase 3 were determined in vivo by generating three genetically modified lysyl hydroxylase 3 mouse lines. The analysis of these mouse lines demonstrated that lysyl hydroxylase 3 possesses at least lysyl hydroxylase and glucosyltransferase activities in vivo and it functions as the main, if not the only glucosyltransferase during embryogenesis. The absence of lysyl hydroxylase 3 and, especially, its glucosyltransferase activity results in the abnormal glycosylation of type IV collagen, and thus causes a severe basement membrane defect leading to death during early development. By contrast, lysyl hydroxylase activity had no effect on embryonic development, but caused changes in the structure of the epidermal basement membrane and changes in collagen fibril organization and probably in their interactions.

Abstract HIF prolyl 4-hydroxylases (HIF-P4Hs) and HIF asparaginyl hydroxylase (FIH) are novel members of the 2-oxoglutarate dioxygenase family that play key roles in the regulation of the hypoxia-inducible transcription factor (HIF). They hydroxylate specific proline and asparagine residues in HIF-α, leading to its proteasomal degradation and inhibition of its transcriptional activity, respectively. These enzymes are inhibited in hypoxia, and as a consequence HIF-α becomes stabilized, forms a dimer with HIF-β, attains its maximal transcriptional activity and induces expression of many genes that are important for cell survival under hypoxic conditions. The three HIF-P4Hs and FIH were expressed here as recombinant proteins in insect cells and purified to near homogeneity. All these enzymes were found to require long peptide substrates. The three HIF-P4Hs and FIH acted differently on the various potential hydroxylation sites in the HIF-α isoforms. The HIF-P4Hs acted well on sequences with cores distinctly different from the core motif -Leu-X-X-Leu-Ala-Pro-, suggested based on sequence analysis studies, the alanine being the only relatively strict requirement in addition to the proline itself. Acidic residues around the hydroxylation site also played a distinct role. These results together with those of others provide evidence that there is no conserved core motif for the hydroxylation by HIF-P4Hs. The Km values of the HIF-P4Hs for O2 were slightly above its atmospheric concentration, while the Km of FIH was about one-third of these values but still 2.5 times that of the type I collagen P4H. The HIF-P4Hs are thus effective oxygen sensors, as even small decreases in the amount of O2 affect their activities, while a more severe decrease is required to inhibit FIH activity. Small molecule inhibitors of the collagen P4Hs also inhibited the HIF-P4Hs and FIH but with distinctly different Ki values, indicating that it should be possible to develop specific inhibitors for the HIF-P4Hs and FIH. The HIF-P4Hs were found to bind the iron cosubstrate more tightly than FIH and the collagen P4Hs, and the chelator desferrioxamine was an ineffective inhibitor of the HIF-P4Hs in vitro. Several metals were effective competitive inhibitors of FIH but they were ineffective inhibitors of the HIF-P4Hs. The well-known stabilization of HIF-1α by cobalt and nickel is thus not due to a simple competitive inhibition of the HIF-P4Hs, and is probably at least in part due to HIF-P4H-independent mechanisms. The effective inhibition of FIH by these metals nevertheless indicates that the stabilized HIF-1α is transcriptionally fully active.

Yes / Studies on the substrate selectivity of recombinant ferrous-iron- and 2-oxoglutarate-dependent proline hydroxylases (PHs) reveal that they can catalyse the production of dihydroxylated 5-, 6-, and 7-membered ring products, and can accept bicyclic substrates. Ring-substituted substrate analogues (such hydroxylated and fluorinated prolines) are accepted in some cases. The results highlight the considerable, as yet largely untapped, potential for amino acid hydroxylases and other 2OG oxygenases in biocatalysis.

The flavonols are a varied and abundant sub-class of flavonoids that are associated with a number of essential physiological functions in plants and pharmacological activities in animals. The 2-oxoglutarate-dependant dioxygenases(2-ODDs), flavonol synthase (FLS) and flavanone 3-hydroxylase (F3H), are essential for flavonol synthesis. The primary goal of this study has been to gain a deeper understanding of the biochemistry of these enzymes in Arabidopsis. To accomplish this goal, an activity assay employing recombinant protein expression and HPLC as a detection system was developed for F3H and adapted for use with FLS. The assay was employed to establish the biochemical parameters of F3H from Arabidopsis, and to further characterize the F3H mutant allele, <i>tt6</i>(87). Enzymatic activity was demonstrated for F3H enzymes from <i>Ipomoea alba</i> (moonflower), <i>Ipomoea purpurea</i> (common morning glory), <i>Citrus sinensis</i> (sweet orange), and <i>Malus X domestica</i> (newton apple), each of which had previously been identified solely based on sequence homology. Arabidopsis contains six genes with high similarity to <i>FLS</i> from other plant species; however, all other central flavonoid pathway enzymes in Arabidopsis are encoded by single genes. The hypothesis that differential expression of FLS isozymes with varying substrate specificities is responsible for observed tissue-specific differences in flavonol accumulation was tested. Sequence analysis revealed that <i>AtFLS2, 4</i> and <i>6</i> contain premature stop codons that eliminate residues essential for enzyme activity. AtFLS1 was found to have a strong preference for dihydrokaempferol as a substrate. However, no enzyme activity was observed for AtFLS3 or AtFLS5 with a number of different substrates under a variety of reaction conditions. To identify structural elements that may contribute to the observed differences in biochemical activity, homology models for each of the isoforms were generated utilizing Arabidopsis anthocyanin synthase (ANS) as a template. A domain at the N-terminus of AtFLS1 that is missing in the other isozymes was insufficient to convey activity to an AtFLS1/5 chimera. These findings suggest a single catalytically-active form of FLS exists in Arabidopsis. The possibility that the apparently expressed but non-catalytic proteins, AtFLS2, 3, and 5, serve noncatalytic roles in flavonol production were explored by yeast 2-hybrid analysis. / Ph. D.

The pharmacologically important alkaloids morphine and codeine are found in latex of opium poppy (Papaver somniferum). Latex is harbored in laticifers, a specialized vascular cell-type. Isolation and characterization of latex-specific genes may provide a useful tool to metabolically engineer increased alkaloid production. Previous research in the Nessler laboratory identified genes that exhibit latex-specific gene expression. Latex-specific genes were an 2-oxoglutarate-dioxygense (DIOX), involved in hydroxylation, desaturation and epoxidation reactions, and two of the major latex proteins, MLP146 and MLP149. MLP-like proteins function in fruit ripening in various species that do not have the laticifer cell type. The latex-specific promoters (LSPs) for the three genes were sequenced. The 2.5 kb DIOX promoter was fused to the reporter gene &#914;-glucuronidase (GUS) to characterize its expression pattern. To assess the functional sites within the DIOX promoter, deletions were made 1.5 kb and 0.14 kb upstream of the ATG start codon, fused to GUS, and transformed into opium poppy, Arabidopsis thaliana, and tobacco (Nicotiana tabacum). The 2.5 kb DIOX:GUS and 1.5 kb EcoRIDIOX:GUS reporter gene constructs showed vascular specific expression in opium poppy, Arabidopsis, and tobacco. The 0.14 kb SpeIDIOX promoter deletion construct showed no activity in opium poppy, and limited expression in the shoot apical meristem and root hypocotyl axis in Arabidopsis. These results indicate that the minimum active DIOX promoter is greater than 0.14 kb. Over 1 kb of the LSPs were sequenced and analyzed for regulatory elements using the Plant cis-acting regulatory DNA elements database, PLACE (http://www.dna.affrc.go.jp/PLACE). Knowledge of the cis-elements and regulatory regions of LSPs would serve as a tool for metabolic engineering of poppy alkaloids. Sixty-five elements were conserved among 2 of the 3 LSPs. Among the cis-elements identified, some are associated with basic functions such as: light regulation, carbon metabolism and plant defense. Other elements include: WRKY elements that are binding sites of transcription factors known for signaling plant defense genes, a vascular cis-element, and a fruit specific element. The presence of plant defense and vascular cis-elements in the LSPs, correlate with the concept that latex is a protective defense mechanism found in the vascular system. The latex-specific promoters isolated and cis-elements identified in this research are potential tools for driving increased alkaloid production in opium poppy. / Master of Science