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<p>In plants, S-adenosyl-L-methionine-dependent phospho-base <em>N</em>-methyl transferases catalyze the three sequential methylations of phosphoethanolamine to phosphocholine, the precursor for choline and the major membrane phospholipid phosphatidylcholine. The enzyme phosphoethanolamine <em>N</em>-methyltransferase (PEAMT) catalyzes the first and committing step in choline synthesis, a step for which no known by-pass has been found. In <em>Arabidopsis thaliana</em> there are two loci annotated as encoding PEAMT and a putative PEAMT, At3g18000 (<em>NMT1</em>) and<em> </em>At1g73600 (<em>NMT3</em>), respectively. A related gene product that catalyzes the last two methylations is encoded by locus At1g48600 (<em>NMT2</em>). The objective of this study was to investigate the role of <em>NMT3 </em>in <em>Arabidopsis</em>. Three SALK lines carrying independent T-DNA insertions in At1g73600 were used: SALK_062703, SALK_016929c and SALK_120703c.</p> <p>Genomic DNA was used for PCR and sequence analysis of the products established the insertion of T-DNA in the protein coding region of At1g73600 for all three lines. Gene expression was analyzed by q-PCR. Primer design was particularly important for <em>NMT3 </em>transcript quantification by q-PCR. In SALK_062703 <em>nmt3 </em>mutants, the T-DNA is in exon 8 and in the SALK_120703c line it is in intron 6. In both cases, no <em>NMT3 </em>transcripts were detected using primers that annealed to sites 3’ to the position of the T-DNA in the gene. However, low levels of transcripts were detected using primers that annealed at positions 5’ to the site of T-DNA insertion. In the SALK_016929c line the position of the T-DNA insertion was in exon 2 and primers annealing near the site of the T-DNA insertion showed no <em>NMT3 </em>expression in this mutant but amplifying the mid portion of the gene showed WT levels of <em>NMT3 </em>transcripts. Thus all the mutants produce truncated <em>NMT3 </em>transcripts and by avoiding areas that overlap truncated transcript regions we could differentiate between <em>NMT3</em> knock-out or knock-down expression.</p> <p>Wild-type (<em>NMT3</em>) and <em>nmt3 </em>seedlings from the three lines grown on defined media plates showed no difference with respect to primary root length, number or density of lateral roots, and total root length. Exposing seedlings to salt (50 or 75 mM NaCl) led to reductions in root growth but again, roots of wild-type plants were indistinguishable from the mutant seedlings. One anomaly relates to the <em>nmt3</em> SALK_120703c<em> </em>line which showed two root phenotypes. On saline media most of the seedlings had longer roots that resembled the wild-type and other mutant lines and about a third had shortened roots. Whether the seedlings had long or short roots on salt, they all lacked <em>NMT3 </em>transcripts. This line is likely carrying another insertion that yields a salt-sensitive root phenotype. Mutant plants at four-weeks looked like wild-type plants and time of flowering was not reproducibly delayed or accelerated in mutant plants relative to wild-type.</p> <p>In wild-type seedlings the relative expression level of the three <em>NMT </em>genes is similar at day or night with transcript abundance ranked in the order <em>NMT3</em> > <em>NMT2 </em>> <em>NMT1. nmt3 </em>seedlings harvested midday showed no detectable <em>NMT3</em> expression but the abundance of <em>NMT1 </em>transcripts was 6.2-fold and 1.7-fold higher relative to wild-type in shoots and roots, respectively. At night, <em>NMT1 </em>expression in shoots of<em> nmt3 </em>seedlings decreased 4.8-fold relative to the level of <em>NMT1 </em>expression at midday while transcripts detected in roots increased slightly (1.3-fold). Using SALK_036291 <em>nmt1 </em>seedlings we found that <em>NMT3 </em>expression in shoots and roots was modestly up-regulated in the absence of <em>NMT1 </em>expression and the expression of <em>NMT3 </em>is lower at night than during the day. Also, regardless of the genotype or time of day, <em>NMT2 </em>expression remained constant even when <em>NMT1 </em>and <em>NMT3 </em>transcripts underwent several-fold changes in abundance. Interestingly, four-week old <em>nmt3 </em>plants of the SALK_062703 line showed that <em>NMT3 </em>expression is knocked-out in leaves but only knocked-down in roots.</p> <p><em> NMT3 </em>was the most highly expressed of the three <em>NMT </em>genes monitored by q-PCR. Nonetheless, three independent T-DNA insertion lines defective for <em>NMT3</em> expression were wild-type by appearance and as such, offer compelling evidence that NMT3 is not required by <em>Arabidopsis. </em>The increased expression of <em>NMT1 </em>in <em>nmt3 </em>plants and <em>NMT3</em> in <em>nmt1 </em>plants strongly suggests that plants compensate for the loss of one gene by up-regulating, to varying extents, the expression of the remaining <em>NMT </em>gene. If this is the case, a reasonable prediction made for a cross between <em>nmt1 </em>and <em>nmt3 </em>plants is that it would be lethal unless plants have yet another way to circumvent the loss of an essential enzyme for this committing metabolic bottleneck in choline synthesis.</p> / Master of Science (MSc)

<p> Some plants such as spinach, sugar beet, and wheat accumulate the quaternary ammonium compound glycine betaine when exposed to stresses in their environment. Environmental stress can be in the form of an excess or deficiency of water, high salt content, and/or exposure to excessively low or high temperatures and many if not all of these stresses are associated with cell dehydration. </p> <p> Glycine betaine is an organic solute that is believed to help restore the osmotic potential of a cell undergoing dehydration by reducing water loss and preventing damage to the structure and function of macromolecules. However, many plants such as Arabidopsis, tobacco, and rice do not accumulate glycine betaine. Given the perceived benefits of glycine betaine production by plants under stress, studies have been carried out to identify factors regulating its production. </p> <p> Glycine betaine is synthesized by the two-step oxidation of choline. The capacity to synthesize phosphocholine for choline production has been found to limit the production of glycine betaine in non-accumulating plants such as tobacco. As such, genetic engineering has been used to enhance the production of choline to up-regulate the synthesis of glycine betaine. This strategy has required knowledge of the enzyme(s) catalyzing the three N-methylation steps of the phosphocholine biosynthetic pathway. </p> <p> This study focused on a gene product identified as putative-phosphoethanolamine N-methyltransferase (putative PEAMT) based upon its similarity to a spinach Nmethyltransferase known to convert phosphoethanolamine to phosphocholine. This gene is located at the locus Atlg73600 on chromosome I of Arabidopsis and its predicted amino acid sequence has high similarity to two other genes encoding N-methylating enzymes located at At3 g 18000 (a biochemically confirmed PEAMT) and At 1 g48600 (annotated as a putative PEAMT). </p> <p> In this study, publicly available microarray data was examined to identify an expression profile of transcripts associated with the Atlg73600 gene in organs and tissues of Arabidopsis at various developmental stages. A summary of the micro array data shows the highest abundance of transcripts for Atlg73600 to be in the rosette leaves of Arabidopsis at 18.0- 20.9 days of growth. </p> <p> Arabidopsis plants grown from seeds from four SALK lines reported to have a TDNA insert in the Atlg73600 gene were screened for the presence of a T-DNA tag using a three primer PCR design strategy. Individual plants from two of the lines were found to have a T-DNA insert present. RT-PCR was then used to analyze the expression of transcripts associated with the Atlg73600 gene in these mutant lines. Transcripts were not detected among the amplified products from eDNA produced from the SALK line designated 062703 but they were found at reduced levels in eDNA of SALK line 016929c. </p> <p> In future studies the two T -DNA mutant lines identified in this study can be used to assign a biological role for the product of the Atlg73600 gene by examining the phenotype of these mutant plants relative to that of wild-type plants under normal and/or stressed conditions. The line found with no expression associated with the Atlg73600 gene will be useful in crosses with T -DNA knock-out mutants of genes at loci At3g18000 and Atlg48600. Systematic knock-outs for each of the genes in isolation and in combination will help discern whether there is functional redundancy in their biological roles or if their individual expression contributes uniquely towards the development of a plant or its stress response. Given the associated role for PEAMT in phosphatidylcholine metabolism, lipidomics could be used to determine if the composition of the plant membranes is altered relative to wild-type when the Atlg73600 gene is knocked-out. </p> / Thesis / Master of Science (MSc)

Despite soybean's widespread recognition as a versatile and valuable crop due to many end-use purposes, breeders seek to develop varieties with improved nutritional and functional components that capture added-value for producers. Additionally, producers seek to maximize profits by utilizing field practices to augment crop value. Therefore, this dissertation had two main objectives of maximizing soybean value: 1) to evaluate accelerated selection methods by soybean breeders for methionine content and test weight, and 2) to identify sulfur fertilization impact on soybean seed composition including amino and fatty acid profiles. First, a genome-wide association study (GWAS) analyzed genomic influence on proteinogenic methionine in soybean seeds which identified 23 single nucleotide polymorphisms (SNPs). Utilizing a SNPs subset identified by GWAS, genomic selection (GS) exhibited average prediction accuracies ranging from 0.41-0.62. Secondly, a novel phenomic selection (PS) method using near-infrared reflectance spectroscopy (NIRS) was evaluated for predictive ability of soybean test weight. PS cross-validations exhibited average predictive accuracies of 0.75, 0.59, and 0.16 when incorporating all environments, between locations, and between years, respectively. Finally, sulfur fertilizer rates and sources were assessed across two years and six locations in relation to seed composition. Notably, ammonium sulfate (AMS) was found to have a significant impact (P < 0.05) on methionine content in soybean seed. These outcomes will have positive impacts on plant breeding and soybean production for seed composition and quality traits using contemporary breeding and fertilization. / Doctor of Philosophy / Despite soybean's widespread recognition as a versatile and valuable crop due to a myriad of end-use purposes, breeders seek to develop varieties with improved nutritional and functional components that captured value for producers. Additionally, producers seek to maximize their profits by utilizing field practices that increase crop value. Therefore, this dissertation had two main objectives of maximizing soybean value: 1) to evaluate accelerated selection methods by soybean breeders for methionine content and test weight, and 2) to identify sulfur fertilization impact on soybean seed protein and oil composition. The overall objective was to create a comprehensive toolset for soybean breeders to develop Mid-Atlantic soybean varieties with improved seed composition traits and to determine fertilization impacts for use by producers. Genetic controls for protein-bound methionine in soybean seed were identified and could be used for variety development. Additionally, a new prediction method that uses light reflectance to represent genetic information and environmental effects was shown to have high accuracy for soybean test weight. It was also found that sulfur fertilizer with high availability in the soil positively impacted methionine content. These outcomes will have positive impacts on plant breeding and soybean production for seed composition and quality traits using contemporary breeding and fertilization.

Introduction: La sclérose en plaques (SEP) est une maladie inflammatoire et démyélinisante du système nerveux central (SNC). Les lymphocytes T pro-inflammatoires CD4 TH1/TH17 sont considérés pathogéniques en SEP et dans son modèle animal, l'encéphalomyélite auto-immune expérimentale (EAE). La restriction alimentaire en méthionine (MR) est associée à un effet anti-inflammatoire en périphérie. Cependant, l’impact de la disponibilité de la méthionine sur la fonction des lymphocytes T et sur la neuroinflammation centrale médiée par les lymphocytes T dans la SEP et l'EAE n’est pas connu. Il a été récemment découvert que le métabolisme de la méthionine est induit dans les lymphocytes T murins activés in vitro et que la restriction en méthionine affecte les fonctions effectrices et la prolifération des lymphocytes TH17. Nous formulons donc l’hypothèse que la manipulation du métabolisme des lymphocytes T via la restriction diététique en méthionine représente une nouvelle voie thérapeutique pour contrôler les maladies neuroinflammatoires telles que la SEP. Méthode: Des femelles C57BL/6 sont exposées à une diète contrôle ou réduite en méthionine puis immunisées au MOG35-55 pour induire une EAE active. Un suivi clinique et des expériences de cytométrie en flux permettent de caractériser le profil et l’activation immunitaire. Le prélèvement d'échantillons fécaux et le séquençage de l'ARNr 16S permettent d’évaluer l'influence de la diète sur la composition du microbiome intestinal. Résultats: La MR est associée à un délai significatif de l'apparition des déficits neurologiques chez les femelles C57BL/6 immunisées au MOG. Ceci est associé à une réduction du nombre de cellules immunitaires et de lymphocytes T pro-inflammatoires dans la rate au 7e jour post-induction (présymptomatique) et dans le SNC aux jours 10-13 (début) et 15-16 (pic). Nos résultats préliminaires suggèrent que le microbiome intestinal des souris sous la MR est différent de celui des souris sous la MC et est enrichi de bactéries ayant des effets bénéfiques en inflammation. Conclusion: Nos résultats suggèrent un impact bénéfique de la MR sur l'évolution clinique et les processus neuroinflammatoires dans un modèle animal de SEP. / Introduction: Multiple Sclerosis (MS) is an inflammatory and demyelinating disease of the central nervous system (CNS). Pro-inflammatory CD4 TH1/TH17 are considered pathogenic in MS and its animal model, experimental autoimmune encephalomyelitis (EAE). Dietary methionine restriction (MR) is associated with an anti-inflammatory impact in the periphery. However, little is known about how methionine availability can affect the function of T lymphocytes and impact T-lymphocytes mediated central neuroinflammation in MS and EAE. It was recently discovered that methionine pathway is upregulated in activated murine T lymphocytes in vitro and that methionine restriction affects the effector functions and proliferation of TH17 lymphocytes. We therefore hypothesize that the manipulation of T lymphocyte metabolism via the restriction of dietary methionine intake represents a new therapeutic avenue for controlling neuroinflammatory diseases such as MS. Method: Active MOG35-55-EAE is induced in C57BL/6 female mice exposed to low methionine vs. control diet. Clinical evaluation and flow cytometry studies are used to characterize immune cells phenotype and activation. Fecal samples are collected and 16S rRNA sequencing is used to assess the influence of the diet on the composition of the intestinal microbiome. Results: Dietary MR is associated with a significantly delayed onset of neurological deficits in active EAE (female mice). This is paralleled by a lower number of immune cells and pro-inflammatory T lymphocytes in the spleens at day 7 post-induction (presymptomatic) and in the CNS at day 10-13 (onset) and 15-16 (peak). Our preliminary results suggest that the intestinal microbiome of mice under dietary MR is different from that of mice under control diet and is enriched for bacteria with beneficial effects on inflammation. Conclusion: Our results suggest a beneficial impact of MR on clinical course and neuroinflammation in an animal model of MS.

Beneath glycation, oxidation reactions may take place at cereal proteins during production of malt. The extent of oxidative chemical changes at malt proteins has not yet been studied. In the present short communication, malt protein was characterized by the determination of free thiol groups and degree of methionine oxidation as well as the sites that are reactive to covalent modification by 2,4-dinitrophenylhydrazine (DNPH, “protein carbonylation”). Protein carbonylation in pale malts was around 1.5 nmol/mg protein and increased with increasing malt colour. Investigations on the protein pellet isolated for determination of carbonylation revealed that solubility and colour may disturb the quantification of carbonyl sites in roasted malts. Free thiols decreased with increasing malt colour already in pale malts (EBC < 10). The formation of methionine sulfoxide (MetSO) was intensified with increasing malt colour. An amount of 7–20% of methionine was converted to MetSO in pale and dark malt, whereas nearly 60% of methionine was oxidized to MetSO in roasted malts. The formation of methionine sulfone was negligible. This study shows that malt proteins suffer from oxidation during kilning, and future studies will have to show whether this supports the pro- or antioxidant activity of malt.

Les récepteurs couplés aux protéines G (GPCR) sont formés de sept domaines transmembranaires. Cette famille de récepteur fait l'objet d'études qui visent à comprendre leurs fonctions, leurs interactions avec leurs ligands, les changements de conformations produits suite à cette liaison ainsi que leur mécanisme d'activation. Notre hypothèse est que le récepteur humain de l'angiotensine II de type 1 (hAT1 ) possède des déterminants moléculaires responsables de sa liaison à l'angiotensine II (AngII). Nos objectifs sont d'identifier des déterminants moléculaires responsables de sa liaison à AngII, ainsi que d'identifier des changements de conformations générés suite à cette liaison. Dans un premier temps, les déterminants de la liaison de la position C-terminale de l'AngII ont été identifiés directement grâce à des études de photomarquage par affinité sur le récepteur hAT 1. Ces études nous ont permis d'observer que l'acide aminé photoactivable utilisé, le para -benzoyl- L -phénylalanine (Bpa), présentait une sélectivité prononcée pour la méthionine. Nous avons exploité cette sélectivité du Bpa pour mettre au point une nouvelle approche : l'essai de proximité aux méthionines (MPA). Afin de déterminer l'environnement tridimensionnel de la position C-terminale de l'AngII dans le récepteur hATI, nous avons dans un premier temps étudié les domaines transmembranaires (TMD) III, VI et VII en mutant individuellement chacune des positions par une méthionine. Cette étude a permis de déterminer l'orientation relative des résidus identifiés de chaque TMD formant la pochette de liaison. Nous avons fait une étude MPA comparative avec le mutant constitutivement actif N111G-hAT 1 , afin de pouvoir déterminer des changements de hAT1 qui surviennent lors de l'activation, sur les TMD III, VI et VII et avons trouvé qu'une seule différence. La conclusion de l'étude impliquait un mouvement du TMD VI lors de l'activation. Dans une autre étude, les 4 derniers TMD (I, II, IV, V) ont été étudiés à la fois à l'état basal et actif. Cette étude permit d'identifier que les TMD II et V participent à la formation de la pochette de liaison de l'AngII dans la forme active uniquement, impliquant des mouvements dans ces 2 TMD aussi. Suite à l'identification des résidus des TMD participant à la structure de la pochette de liaison, dans la forme active ou inactive, nous avons construit des modèles du récepteur hATI ligandé dans la forme inactive et de la forme constitutivement active et les avons comparés. L'ultime but de ce projet est de présenter un modèle d'activation général des GPCR mais plus concrètement une meilleure compréhension des bases moléculaires de la liaison, de l'activation et des changements conformationnels d'un GPCR.

O estado de metilação é suscetível a mudanças quando os organismos são expostos a agentes ambientais tais como componentes dos alimentos e medicamentos. Uma dieta rica em metionina (Met) poderia modular a concentração de S-adenosilmetionina (SAM) e S-adenosilhomocisteína (SAH) e alterar o estado de metilação da região promotora de genes supressores de tumores. Tanto a hipometilação global quanto a hipermetilação de genes específicos estão envolvidas na instabilidade genômica e poderiam resultar em dano ao DNA. Este estudo avalia se a dieta suplementada com Met associada a doxorrubicina (DXR), um fármaco antitumoral que induz espécies reativas, resulta em alterações no estado de metilação da região promotora do gene TP53, na razão SAM/SAH, na concentração de glutationa (GSH) e em dano ao DNA. Quarenta ratos machos Wistar foram separados em dois grupos: dieta suplementada com Met (ração comercial acrescida de 2% Met) e dieta controle (ração comercial) por seis semanas. Cada grupo foi subdividido em dois subgrupos que receberam DXR (1mg/Kg) ou solução salina intraperitoneal na terceira e sexta semanas de tratamento. Os rins e fígado foram utilizados para isolamento do DNA, determinação da concentração de SAM, SAH e GSH, e análise da instabilidade genômica. Todos os grupos apresentaram o mesmo estado de metilação da região promotora do gene TP53, determinado pelo método de análise de restrição combinada com bissulfito (COBRA). Este fato poderia ser explicado pelo índice de metilação (razão SAM/SAH) que permaneceu inalterado, possivelmente devido a uma adaptação do ciclo da Met que manteve a concentração de SAM. A depleção de GSH não ocorreu quando DXR foi associada a dieta suplementada com Met. Portanto, a suplementação com Met manteve a concentração de GSH em ratos tratados com DXR. A dieta suplementada com Met não induziu instabilidade genômica e não alterou o dano ao DNA induzido pela DXR. Em conclusão, DXR induz depleção de GSH que é inibida pela suplementação com Met. Entretanto, a mesma suplementação não previne a instabilidade genômica induzida pela DXR. A dieta suplementada com Met aumenta a concentração de SAH renal sem alterar a concentração de SAM e GSH. Tanto a dieta suplementada quanto a DXR não induzem hipermetilação na região promotora do gene TP53. / The DNA methylation status is susceptible to changes when organisms are exposed to environmental agents such as food components and drugs. A methionine-rich (Met) diet may modulate S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) concentrations, which could change the DNA methylation status in the promoter region of tumor suppressor genes. Global hipomethylation and gene-specific hipermethylation are involved in genomic instability and it could result in DNA damage. This study intends to evaluate if a Met-rich diet associated with doxorubicin (DXR), an antitumoral drug that induces reactive species, result in changes in the methylation status of the TP53 gene promoter, in the SAM/SAH ratio, in glutathione levels (GSH) and in DNA damage. Forty male Wistar rats were separated into two groups: Met-rich diet (standard chow plus 2% Met), and control diet (standard chow) for six weeks. Each group was subdivided into another two groups that received DXR (1mg/kg) or saline intraperitoneally in the third and sixth weeks of the experiment. The kidneys and the liver were removed for DNA isolation, SAM, SAH and GSH determination, and genomic instability assay. All groups showed the same unmethylated status in the TP53 promoter according to the Combined Bisulfite Restriction Analysis (COBRA). This could be explained by the fact that the methylation index (SAM/SAH ratio) remained unchanged, possibly because of an adaptive Met pathway that maintains SAM levels. GSH depletion did not occur when DXR was associated with the Met-rich diet. As a matter of fact, the Met-rich diet improved GSH concentration in DXR-treated rats. Met-rich diet did not induce genomic instability, and it did not alter DNA damage induced by DXR. In conclusion, DXR induces GSH depletion which is inhibited by Met supplementation. However, Met-rich diet may not prevent genomic instability induced by DXR. A Met-rich diet increases SAH levels; however, it does not change GSH and SAM levels. Neither Met supplementation nor DXR induced DNA hypermethylation in the TP53 gene promoter.