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Individual isolates of the fungus Nectria haematococca exist in a wide range of habitats and part of this diversity is attributed to the presence of conditionally dispensable (CD) chromosomes that carry habitat-defining genes. In the current study a new factor located on one of these CD chromosomes was found. This trait allows pea pathogenic isolates of N. haematococca to grow in homoserine, a compound present in large amounts on pea root exudates. The gene(s) for homoserine utilization (HUT) are located on the same CD chromosome that carries the cluster of genes for pea pathogenicity, the PEP cluster. The PDA1 gene, a member of the PEP cluster, is routinely used as a marker for the presence of this CD chromosome, therefore it has been called the PDA1-CD chromosome. For the purpose of identifying the HUT gene(s), a physical map of the PDA1-CD chromosome was constructed. This map, in combination with synteny analysis, and Southern hybridizations led to the identification of a region of 365Kb that is likely to contain the HUT gene. By searching the publicly available genome of N. haematococca several candidates for HUT were identified.The synteny evaluation between the PDA1-CD chromosome and a different CD chromosome that carries the MAK1 gene, for chickpea pathogenicity, revealed a region (> 463Kb) of synteny, which advocates for a common ancestor for these CD chromosomes. However a large region (~ 1 Mb) in each of the CD chromosomes was found to carry unique DNA, therefore we proposed that individual isolates of this fungus contain large regions of unique DNA located on the CD chromosomes. The localization of syntenic regions also suggests that breakage points previous identified in the MAK1-CD chromosome could potentially be "hot spots" for recombination between both CD chromosomes. Furthermore, the anchoring of the PDA1-CD map to the genome of N. haematococca allowed the identification of additional putative habitat colonization genes present on both CD chromosomes, and niche-defining genes on the PDA1-CD chromosome.

Gram-negative bacteria use N-acyl homoserine lactones (AHLs) to sense population density and regulate gene expression, including virulent phenotypes. The quorum-quenching AHL lactonase from Bacillus thuringiensis cleaves the lactone ring of AHLs, disabling this mode of gene regulation. Despite the potential applications of this enzyme as an antibacterial weapon, little was known about it's lactone ring-opening mechanism. As a member of the metallo-beta-lactamase superfamily, AHL lactonase requires two divalent metal ions for catalysis. NMR experiments confirm that these metal ions are also involved in proper enzyme folding. The chemical mechanism of ring opening was explored using isotope incorporation studies, and hydrolysis was determined to proceed via a nucleophilic attack by a solvent-derived hydroxide at the carbonyl of the lactone ring. A transient, kinetically significant metal-leaving group interaction was detected in steady-state kinetic assays with AHL lactonase containing alternative divalent metal ions hydrolyzing a sulfur-containing substrate. High-resolution crystal structures implicated two residues in substrate binding and hydrolysis, Tyr194 and Asp108. Site-directed mutagenesis of these residues followed by steady-state kinetic studies with wild-type and mutant enzymes hydrolyzing a spectrum of AHL substrates revealed that mutations Y194F and D108N significantly affect catalysis. Combining these results allows the proposal of a detailed hydrolytic mechanism. The binding site for the N-acyl hydrophobic moiety was probed using steady-state kinetics with a variety of naturally occurring and non-natural AHL substrates, and these studies indicate that AHL lactonase will accept a broad range of homoserine lactone containing substrates. Crystal structures with AHL substrates and non-hydrolyzable analogs reveal two distinct binding sites for this N-acyl group. Based on the ability of this enzyme to accommodate a variety of substrates, AHL lactonase was shown to have the ability to quench quorum sensing regulated by a newly discovered class of homoserine lactone signal molecules possessing an N-aryl group using a bioassay. Steady-state kinetic studies confirm that this class of signal molecules are indeed substrates for AHL lactonase. / text

Thiamine-phosphate kinase (or ATP:thiamine-phosphate phosphotransferase, ThiL) and homoserine (ThrB) kinases are essential to metabolism in Mycobacterium tuberculosis (Mtb). ThiL and ThrB respectively phosphorylate thiamine monophosphate (TMP) to thiamine diphosphate (TDP), the active form of vitamin B1, and L-homoserine to Ophosphohomoserine, critical to aspartate biosynthesis. In this study, ThiL and ThrB from Mtb were characterised structurally and functionally by producing the proteins recombinantly in E. coli. Proteins were purified by affinity, anion exchange and size exclusion chromatographies and purity checked by SDS-PAGE. ThiL and ThrB enzyme activities were confirmed and reaction products verified by high pressure liquid chromatography (HPLC). The crystal structure of ThiL was solved by molecular replacement using X-ray diffraction data. Functionally active ThiL, 36 kDa, produced hexagonal crystals belonging to space group P6122 with one monomer per asymmetric unit. Structurally it is related to ThiL from other organisms with minor structural deviations. Enzymatically active ThrB, 33 kDa, was crystallised. However, crystals failed to diffract Xrays to a suitable resolution. ThiL and ThrB could act as possible anti-TB drug targets against Mtb. / Dissertation (MSc)--University of Pretoria, 2017. / Biochemistry / MSc / Unrestricted

Chez les Vibrio spp., le QS est impliqué dans de nombreuses fonctions comme la colonisation de niche écologiques, les stratégies de survie ou encore la virulence. Cependant, pour la majorité des espèces de Vibrio, la diversité des AHLs produites reste largement sous-estimée et l'étude du QS est encore limitée à quelques espèces modèles ou pathogènes. Toutefois, dans les environnements aquatiques, ces espèces sont minoritaires et les espèces les plus abondantes ne sont que très peu étudiées. Nos résultats ont révélé une importante diversité d'AHLs mais aussi, de façon surprenante, une hétérogénéité dans les phénotypes de production d'AHL au sein d'une même espèce de Vibrio. Pour la première fois, nous avons mis en évidence qu'une même souche de Vibrio pouvait présenter des phénotypes de production d'AHLs différent au cours du temps et une approche statistique a révélé l'implication de certains déterminants biotiques et abiotiques dans ces variations temporelles. Par ailleurs, une approche à micro-échelle a révélé une structuration des populations de Vibrio en unités fonctionnelles constituées de souches phylogénétiquement proches qui partagent des niches écologiques spécifiques et des comportements sociaux. Nos résultats ont mis en évidence que les modalités de communication pouvaient être hétérogènes suggérant l'absence d'un langage commun au sein de ces unités fonctionnelles. En conclusion, ce travail de thèse a permis d'apporter de nouvelles connaissances sur le QS chez les Vibrio dans l'environnement marin, de la souche à la population, et propose une vision intégrée des mécanismes de régulation de la production d'AHLs dans l'environnement. / Quorum sensing is an important mechanism among Vibrio species and is involved in many vital functions such as niche colonization, survival strategies or virulence. However, AHL diversity still largely underestimated for the majority of Vibrio species and the current knowledge on AHL-mediated QS is limited to a few pathogenic or bioluminescent species. Nonetheless, these species are weakly abundant in seawater while dominant species in the environment are poorly studied. Our results revealed a unexpected diversity of AHL molecules but also a quite surprising intra-species diversity of AHL production phenotypes. For the first time, we showed that different isolates of a single genotype switched between different AHL production phenotypes among time and we revealed the potential involvement of abiotic and biotic parameters in these variations. However, it appears that when studied at a microscale, Vibrio populations are showing a functional structuration in ecological units consisting of phylogenetically close strains sharing habitat and social traits. In this context, it was necessary to determine if these different AHL production phenotypes were associated to different micro-habitats in the water column. We did not demonstrate that a common language was spoken within ecological populations. This thesis work provide new insights on AHL-mediated QS among a broader range of species and among Vibrio populations and depicts the potential impact of multiple aspects of marine environments on AHL production.

Les bactéries sont capables de communiquer entre elles afin de coordonner l’expression de certains gènes en fonction de leur densité de population. Ce système de communication utilise de petites molécules appelées autoinducteurs (AIs) comme messagers chimiques et est connu sous le nom de Quorum Sensing (QS). Chez les bactéries pathogènes, les gènes régulés sont, en particulier, ceux codant pour la production des facteurs de virulence et la structuration des biofilms. Ainsi des inhibiteurs du QS chez ces bactéries pourraient être de nouveaux agents anti-bactériens alternatifs aux antibiotiques actuels. Chez les bactéries à Gram-négatif, les AIs sont très majoritairement des acyl-homosérine lactones (AHLs). Utilisant deux approches, la conception rationnelle et le criblage virtuel, nous avons découvert cinq nouvelles familles d’antagonistes des AHLs, ainsi qu’un certain nombre d’agonistes. Nous avons également préparé des analogues d’antagonistes naturels de la famille des bromo-furanones, afin d’établir une étude structure-activité de ce type de composés. / The bacteria are able to communicate with each other for coordinating gene expression depending on their population density. This communication system use small molecules called autoinducers (AIs) as chemical messengers and is referred to as quorum sensing (QS). In pathogenic bacteria, the regulated genes are, in particular, those coding for the production of virulence factors and biofilms formation. Thus, inhibitors of bacterial QS could be used as new anti-bacterial agents providing an alternative to current antibiotics. In Gram-negative bacteria, the main AIs are acyl-homoserine lactones (AHLs). Using two approaches, rational design and virtual screening, we have discovered five new families of AHLs antagonists, and some agonists. We have also prepared analogues of natural bromo-furanones antagonists, in order to establish a structure-activity study of this type of compounds.

A semente de milho, base da alimentação em muitos países na África, Ásia e América Latina, possui ~10% de proteína na semente. Por ser um cereal a proteína da semente de milho apresenta uma baixa concentração de aminoácidos essenciais como: lisina e triptofano. Com a descoberta do milho opaco-2, o qual apresenta um maior teor de lisina e triptofano em suas sementes, surgiu a oportunidade de se desenvolver milhos com qualidade protéica, aumentando o conteúdo de aminoácidos e a qualidade nutricional dos grãos. Assim, surgiu o milho QPM (quality protein maize), milho de alta qualidade protéica, melhorado pelo CIMMYT (México). O QPM possui duas vezes mais lisina que o milho normal mantendo a sua produtividade equivalente. A EMBRAPA, Milho e Sorgo, desenvolveu duas variedades QPM comercializadas: BR451 e BR473. A linhagem QPM 161 (EMBRAPA Milho e Sorgo) teve suas proteínas de reserva analisadas bioquimicamente neste trabalho, concluindo que o QPM 161, possui uma concentração maior de lisina em suas sementes, chegando a superar o BR 451 e a manter a mesma concentração de lisina que o BR 473. Em outra parte do trabalho, sementes imaturas (14, 20 e 14 DAP) das linhagens 161, assim como as do selvagem W22+ e de seus mutantes W22o10, W22o11 e W22o13, foram utilizadas para caracterizar a enzima homoserina quinase (HK). A HK faz parte da via de biossíntese do aminoácido essencial treonina. Constatou-se que uma alta atividade desta enzima está relacionada ao aumento de treonina na semente, porém, a alta atividade de HK foi observada nos menores estágios de maturação. Assim os resultados mostram que mais estudos sobre a regulação desta enzima devem ser realizados para que se possam desenvolver sementes ricas em lisina e também em treonina. / Maize which is the staple food in many countries in Africa, Asia and Latin America, has ~10% of protein in the seeds. Maize seeds protein presents low contents of essential amino acids, such as lysine and tryptophan. Since the discovery of the opaque-2 maize, a recessive mutation that results in high concentrations of lysine and tryptophan, the major challenge has been to develop better quality protein maize to increase the rate of amino acids consumed by population. The QPM (quality protein maize), originally produced and breeded at CIMMYT in Mexico, came to solve the issue. The QPM protein has twice as much lysine and tryptophan, with the same yield of normal maize. The EMBRAPA, Maize and Sorghum, has bred two QPM varieties that are already commercialized (BR 451 and BR 473), but to increase the quality of the Brazilian QPM, EMBRAPA developed a new QPM line, the 161, whose storage proteins were biochemically analyzed in this study. Line 161 exhibited a higher lysine concentration than BR 451, but about the same concentration of that exhibited by BR 473. Further analyses conducted in this research involved the study of immature seeds (14, 20 and 24 DAP) of line 161, and the wild-type W22+ and its counterpart mutants W22o10, W22o11 and W22o13, and the characterization of the enzyme homoserine kinase (HK). HK is a key enzyme of the threonine biosynthetic pathway. The high HK activity was shown to be related to the increased threonine concentration in the maize seeds. HK activity was shown to reach the highest level in the first developmental stage, whereas in the last developmental stage the activity is lower and so is the rate of threonine. Therefore, it is necessary more studies on HK regulation to improve the mature maize seeds with the best rate of lysine and threonine.