Thesis (MSc (Biochemistry))--University of Stellenbosch, 2005. / This study describes: 1. The cloning of baboon cytochrome P450 side-chain cleavage (CYP11A1) cDNA by in vitro site-directed mutagenesis. 2. The identification and sequencing of three baboon CYP11A1 mutants: CYP11A1a, CYP11A1b and CYP11A1c. 3. The expression and characterisation of baboon and human CYP11A1 cDNA, CYP11A1a, CYP11A1b and CYP11A1c in nonsteroidogenic COS-1 cells. The Km and V-values for the metabolism of 25-hydroxycholesterol were determined. 4. The construction of the first homology model of CYP11A1, using both mammalian (CYP2C5) and bacterial (CYP102) cytochromes P450 crystal structures as templates. 5. A structure/function study into the role of the amino acid residues Ile98, Lys103 and Thr291 in substrate binding and enzymatic activity. 6. The proposal of a topological model of the CYP11A1 active pocket as determined by substrate docking studies.

Weed infestation is one of the yield limiting factors in crop production. Weeds have negative effect on crop growth and productivity due to competition, allelopathy or hosting other harmful organisms. For large-scale wheat production, the use of wide spectrum pre-emergence or post-emergence herbicides remains the most valuable weed control tool. In South Africa, annual grass weeds are a major wheat production constraint, which is usually managed through application of pre-emergence herbicides. Due to limited water availability and low soil moisture content, these herbicides can often become ineffective and result into high weed infestations, which then have to be managed by manual cultivation or post-emergence herbicidal applications. However, there are no effective selective post-emergence herbicides available to control grass weeds in wheat. There is also limited option to use broad-spectrum post-emergent herbicides because they non-selectively kill the crop and weeds. Consequently, the use of herbicide resistant crops is a viable weed management system in wheat production. Breeding herbicide resistant crop varieties would allow farmers to safely use post-emergence herbicides without damaging the crop. Subsequently yield and quality losses will be reduced significantly. Thus, the development of herbicide resistant crop varieties through mutation breeding is a novel approach for effective weed management under both small-scale and commercial farmers. Mutagenesis has been recognized as one of the most efficient method to induce genetic variation in plants. Through induced mutations, development of new variants is possible that could be manipulated in plant breeding programs. Mutation leads to alteration of various traits in crop plants including plant height, improved nutritional quality, shorter growing period, increased tolerance or resistance to abiotic and biotic stresses. Ethylmethanesulphonate (EMS) is one of the most widely used chemical mutagens to induce mutagenesis in crop plants. The objectives of this study were to: 1) determine the optimum EMS concentration, treatment temperature and duration that would provide desired germination percentage and vigorous and healthy seedlings for effective mutagenesis in wheat, 2) investigate variations in agro-morphological traits in two selected wheat varieties (SST56 and SST875) after EMS mutagenesis and 3) select herbicide resistant wheat germplasm after inducing genetic variation using EMS using two selected wheat varieties (SST56 and SST875). The objectives were achieved through three independent studies as outlined below: In the first study seeds of four selected wheat varieties (B936, B966, SST387 and SST875) were treated in two replicates with three EMS concentrations (0.3, 0.5, and 0.7%), three temperature regimes (30, 32.5 and 35 °C) at four time durations (0.5, 1, 1.5 and 2 hrs). Results showed highly significant interactions (P<0.01) among varieties, EMS concentrations, temperature and exposure time on seedling emergence, germination and seedling height. Seeds treated with the highest EMS dose (0.7%), temperature (35ºC) and long exposure time (2 hr) showed delayed emergence by 18 days. At 30ºC, 0.5hr and 0.3% EMS varieties B936, B966 and SST875 had early emergence (6 days). B936 and SST387 had 50% while B966 and SST875 had 53% and 57% germination, respectively. These results were observed at EMS level of 0.7%, 300C and 1.5 hr exposure time in B936 and EMS at 0.5%, 350C and 1.5 hr in B966. SST387 and SST875 required EMS dose at 0.5%, 32.50C and 2 hr treatment time. Other low or high treatment combinations were invariably ineffective comparedto untreated control. During the second study two selected varieties (SST56 and SST875) were subjected to EMS mutagenesis using 0.5% v/v EMS at 32.5oC for 1 hr. Field trials were carried out at Ukulinga research farm of the University of KwaZulu-Natal in the randomized complete block design with two replicates. Data on nine important agro-morphological traits were collected and analyzed using the analysis of variance (ANOVA), correlation and principal component analysis (PCA) procedures. Significant variations were found among the agro-morphological traits between M1 individuals compared to untreated checks. The mutagenesis significantly reduced seed germination in the field at 40% in both varieties. The treatment significantly delayed days to heading by 8 days and shortened days to maturity by 13 days in both varieties. EMS treatment also significantly reduced plant height at 18 cm in SST56 and 21 cm in SST875 and spike length reduced by ~2.5 cm in both varieties. Plant height had positive and significant correlation with number of tillers, number of seeds per spike, flag leaf length and 100 seed weight. However, it had negative correlation with the number of days to maturity. The PCA revealed that three principal components (PC1, PC2 and PC3) accounted to 57% of the total variations among the agro-morphological traits in both varieties. PC1 alone contributed to 27.7% of the variation which was well-correlated with plant height (0.767), tiller number (0.812), number of seeds per spike (0.599) and seed yield (0.720). PC2 explained 15.6% of the variation and well-correlated with germination percentage (0.784), spike length (0.554) and flag leaf length (0.772). PC3 accounted to 12.4% of the variation and had negative correlation with days to maturity (-0.730). In the last study, seeds of two selected wheat varieties (SST56 and SST875) were treated with EMS at 0.5% concentration for 2 hr at 32.5ºC. Treated seeds and comparative controls were planted at the experimental farm of the University of KwaZulu-Natal using the randomized complete block design. Four weeks after planting M1 plants and untreated standard checks were sprayed with two herbicides, i.e. metsulfuron-methyl and bromoxynil at three different doses viz. 2x, 4x and 8x above the recommended rate of 4 g ha-1 and 2 kg ha-1, respectively. Two weeks after the treatment herbicide resistance were assessed. Results showed significant difference among varieties, tested herbicides and doses used. The EMS treated wheat lines showed variable degree of herbicide resistance compared to untreated controls. Overall, the study established the requirement of variety specific EMS dose and treatment temperature and duration that could be used for inducing large-scale mutation to select targeted mutant individuals in wheat. Further, the study found that EMS has the potential to increase agro-morphological variations in wheat to select useful and novel mutants with desired phenotypic traits and herbicide resistance which will be subjected for further selections to identify stable and herbicide resistance lines. / Thesis (M.Sc.Agric.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.

The described experimental model of clonal tumors induced through the insertional mutagenesis with MAV-2 proved to be a valid and rich source of information describing the process of transformation of normal into tumor cell. We have mapped more than 2000 individual clonal VISs from several hundreds of tumor tissue samples. We have analyzed five tumor types of different histology and tissue of origin along with their derivative tissue cultures. Furthermore, we have discovered the industasis phenomenon and described it during the course of the study. The goal of my study was to uncover common reasons for neoplastic transformation of the cell. The results of my study led me to the paradoxical conclusion that the significance of genetic changes as the primary cause of induction of neoplastic transformation is being overestimated. Although studying the functions of individual genes and search for new tumor markers and therapeutical targets are still beneficial, I believe that the traditional perception of tumor formation as a function/result of mutation accumulation and selection is becoming a serious drawback in further investigations. These conclusions are further discussed in the last section of the presented Ph.D. thesis.

Leptosphaeria maculans est un Dothideomycète phytopathogène capable d’alterner des modes de vie saprophyte, hemibiotrophe endophyte et nécrotrophe durant son cycle infectieux sur le colza. Afin de comprendre cette plasticité infectieuse, une mutagenèse aléatoire à grande échelle par ATMT a permis de générer une collection de 5000 transformants. L’objectif principal de cette thèse était d’exploiter cette collection en prenant avantage de la disponibilité d’outils de génomique, pour, d’une part, comprendre les mécanismes d’intégration de l’ADN-T dans le génome, et d’autre part, identifier des déterminants du pouvoir pathogène ciblés par l’ADN-T dans des mutants affectés dans leur capacité infectieuse. Une analyse systématique de 318 pieds d’insertion a été réalisée dans le but de d’évaluer les caractéristiques de l’insertion de l’ADN-T. Ce dernier est fréquemment inséré dans les régions actives riches en gènes, et favorise des gènes impliqués dans des processus biologiques indicatifs d’une conidie germante. Un biais marqué des insertions en faveur des régions régulatrices est observé ainsi qu’une corrélation entre la densité des insertions et le skew CG près du site d’initiation de la transcription. Ces observations sont cohérentes avec le modèle de ciblage intranucléaire de l’ADN-T. Enfin, l’existence de micro-homologies entre le site de pré-insertion et la bordure gauche de l’ADN-T indique une intégration par voie de recombinaison homologue (HR) et/ou microhomologue (MMEJ). Une approche multicritère a été utilisée pour caractériser cette collection. Un test d’inoculation a permis d’identifier 166 mutants altérés dans leur pouvoir pathogène. La validation génétique de la co-ségrégation entre le phénotype altéré et la présence de l’ADN-T indique que 44% des mutants montrant un déterminisme monogénique de l’altération sont effectivement étiquetés. Parmi les mutants altérés, 35 ont été analysé pour : (i) le phénotype de croissance en conditions usuelles de culture et en réponse aux stress oxydatif, UV et nutritif, (ii) le lien entre altération de la germination et pouvoir pathogène. Les gènes affectés par l’intégration de l’ADN-T, ont été identifié et analysé dans la souche sauvage à l’aide de données de transcriptomique. Ces cribles ont permis de décomposer le phénotype d’altération in planta en plusieurs phénotypes in vitro. Le plus fréquemment, les mutants ne sont pas altérés dans leur in vitro croissance, mais la plupart sont sensibles aux ROS. Les analyses d’expression au cours de l’infection indiquent que les gènes codant pour des effecteurs et ceux impliqués dans la détoxification des ROS, ont des dynamiques d’expression inverses et bi-phasiques, en lien avec le style de vie hemibiotrophe de L. maculans. Les 42 gènes ciblés par l’ADN-T dans ces mutants ont été identifiés et leur fonction putative disséquée par bioinformatique et transcriptomique. Au final, nous avons identifié six mutants d’intérêt pour une caractérisation fonctionnelle. Deux de ceux-ci deux ont atteint un niveau de caractérisation suffisant pour l’émission d’une hypothèse de travail. Dans le mutant µ1165, l’ADN-T cible un gène codant pour une protéine ribosomale S17 (LmRPS17), dont la régulation dépendrait de la voie de signalisation du complex TORC1. Nos résultats préliminaires suggèrent, d’une part, que TORC1 est une cible potentielle de LmRPS17 et, d’autre part, que la phase biotrophe de l’infection chez L. maculans est probablement régulée par TORC1 via l’enzyme de détoxication des ROS SOD2. Dans le mutant µ444, l’ADN-T cible un gène codant pour un élément rétroviral putatif LmHYP1, largement conservé parmi les ascomycètes. Nos résultats suggèrent que LmHYP1 interviendrait dans la régulation de gènes impliqués dans le pouvoir pathogène, via la production de petits ARN interférents issus hypothétiquement du clivage de son ARN messager par la machinerie de défense anti-rétrovirale. La validation de ces deux hypothèses est en cours au laboratoire. / The Dothideomycete phytopathogen Leptosphaeria maculans is capable to alternate saprophytic, hemibiotrophic, endophytic and necrotrophic life styles during a single infectious cycle on its host plant, Brassica napus. However, little is known about the determinants of such plasticity. As part of a large-scale insertional mutagenesis project aiming at the discovery of pathogenicity factors a collection 5000 transformants has been generated by ATMT. The main objective of my PhD was to take advantage of “omics” to extract biological value from L. maculans mutants collection for a better understanding of T-DNA integration features and further identification of pathogenesis determinants in this fungus. A systematic analysis of 318 T-DNA tags was performed in a large collection of transformants in order to evaluate the features of T-DNA integration in its particular TE-rich compartmentalized genome. The T-DNA integration was mainly targeted to gene-rich, transcriptionally active regions, and favored biological processes that are consistent with the physiological status of a germinating conidia. In addition, T-DNA integration was strongly biased towards regulatory regions, and mainly promoters. Consistently with the T-DNA intranuclear targeting model, the density of T-DNA insertion correlated with CG skew near the transcription initiation site. The existence of microhomologies between promoter sequences and the T-DNA LB flanking sequence was also consistent with T-DNA integration to host DNA mediated by homologous recombination and/or the microhomology-mediated end joining pathways. Based on this data, a multi-criteria approach was used to draw the more possible information from this collection by identifying all 166 mutants reliably affected in pathogenicity, and expanding the genetic analysis. Considering single-gene segregation of the pathogenicity phenotype, our data indicate a 44% ratio of actual tagging. In parallel, for a subset of 35 isolates of the collection, we (i) described growth patterns in regular culture conditions or in response to oxidative, UV or starvation stresses, (ii) evaluated the link between altered germination and pathogenicity, (iii) identified and annotated the genes putatively affected by the T-DNA integration, and (iv) analyzed kinetics of expression of these genes in the WT isolate using available microarrays. Our results showed that pathogenicity alteration phenotype could be broken down into a pattern of phenotypes in vitro including growth, germination defect and susceptibilities to oxidative burst, starvation and UV stresses. Our results showed that most of these mutants were not altered in axenic growth but showed enhanced sensitivity to reactive oxygen species (ROS). Furthermore, our results showed that effectors and ROS scavengers have inverted dynamics during plant infection, consistently with the biphasic hemibiotrophic growth of L. maculans. Also, 42 genes targeted by the T-DNA in these mutants were recovered and dissected. This catalogue allowed us to identify a series of promising mutants for further functional studies. Based on this screening, six mutants were subjected to further analyses but only two reached sufficient advance for hypothesis building. In mutant µ1165, the T-DNA targeted a ribosomal protein S17 (LmRPS17), a downstream component of target of rapamycin complex 1 (TORC1) pathway. Our preliminary results suggested that TORC1 is a potential a target of LmRPS17. Also, biotrophic growth is probably tuned by TORC1 via Super oxide dismutase 2 (SOD2). In mutant µ444, the T-DNA targeted a retroviral-like element LmHyp1 widely conserved among ascomycetes. Our results suggest that LmHyp1 probably acts as a regulatory element during plant infection as its cleavage by the antiretroviral defences is hypothesized to generate siRNAs that silences distant genes. Work on these mutants is in progress.

As fosfolipases A2 (PLA2s, ou fosfatidil-acil hidrolases EC 3.1.1.4) catalisam especificamente a hidrólise das ligações ácido-éster na posição sn-2 de glicerofosfolipídios liberando, como produto da catálise, ácidos graxos e lisofosfolipídio. São encontradas em plantas, mamíferos e em veneno de animais vertebrados e invertebrados e estão envolvidas em uma ampla variedade de processos fisiológicos. A fosfolipase A2 secretada humana do grupo IIA (hsPLA2 gIIA) é uma proteína de fase aguda da resposta imunológica, pois sua expressão é induzida por endotoxinas e citocinas via processos autócrinos e/ou parácrinos durante processos inflamatórios de relevância clínica. A hsPLA2 gIIA mostra efeito bactericida contra infecção por Staphylococcus aureus, e tem marcada preferência por fosfolipídios aniônicos tais como fosfatidilglicerol (PG) encontrados em membranas bacterianas. Uma grande variedade de inibidores de PLA2 do grupo IIA foi descrita na literatura, incluindo substâncias polianiônicas que atuam contra os efeitos inflamatórios destas enzimas. Suramina é um derivado de naftiluréia polissulfonado que recentemente mostrou ligação com os resíduos catiônicos no sítio de reconhecimento interfacial de Bothropstoxina-I (BthTX-I), uma PLA2-Lys49 isolada do veneno de Bothrops jararacussu, inibindo a atividade miotóxica da proteína. Devido ao tipo de interação diferenciada da suramina com BthTX-I em relação aos inibidores competitivos de PLA2, nós avaliamos a especificidade de ligação da suramina na hsPLA2 gIIA como um modelo para estudar este novo tipo de inibidor de PLA2s. O efeito da suramina nas atividades biológicas e de membranas artificiais da hsPLA2 gIIA foi avaliado. A suramina aboliu tanto a atividade hidrolítica da hsPLA2 gIIA quanto a atividade de danificação de membranas artificiais Ca2+ independente. Embora a suramina não tenha inibido a atividade bactericida da hsPLA2 gIIA contra a linhagem Micrococcus luteus, a ativação de macrófagos foi abolida pela mesma de maneira dependente de hidrólise. Além disso, técnicas de simulação de dinâmica molecular, calorimetria de titulação isotérmica e mutagênese sítio dirigida foram utilizadas para mapear os sítios de ligação da suramina na proteína. A interação da suramina com a hsPLA2 gIIA resultou de interações eletrostáticas entre grupos sulfonados com cadeias laterais de aminoácidos da região do sítio ativo e dos resíduos em torno das posições 15 e 116 localizados, respectivamente, na N- e Cterminal. Portanto, estes resultados permitem sugerir que a suramina pode atuar como inibidor de sPLA2s / Suramin is a polysulphonated napthylurea used as an antiprotozoal drug that presents inhibitory activity against a broad range of enzymes. We have evaluated the effect of suramin against the artificial and biological activities of the secreted human group IIA phospholipase A2 (hsPLA2 gIIA), a protein involved in inflammatory processes. To map the suramin binding sites on the hsPLA2 gIIA, proteins with mutations in the active site region and in the protein surface that makes contact with the phospholipids membrane were expressed in E. coli and refolded from inclusion bodies. The activation of macrophage cell line RAW 264.7 by hsPLA2 gIIA was monitored by nitric oxide release, and bactericidal activity of the protein against Micrococcus luteus was evaluated by colony counting and by flow cytometry. The hydrolytic activity of the hsPLA2 gIIA against lipossomes composed of a mixture of dioleoylphosphatidylcholine/dioleoylphosphatidylglycerol (DOPC/DOPG) was inhibited by a concentration of 100 nM suramin. The activation of macrophages by hsPLA2 gIIA was abolished at protein/suramin molar ratios where the hydrolytic activity of the enzyme was inhibited. In contrast, both the bactericidal activity of hsPLA2 gIIA against Micrococcus luteus and permeabilization of the bacterial inner membrane were unaffected by suramin concentrations up to 50 M. The affinity of interaction of the suramin with hsPLA2 gIIA was evaluated by suramine fluorescence and the mutants K15A, K38A, R54A and K123A presented a reduced affinity. The binding of the suramin/hsPLA2 gIIA complex was investigated by molecular dynamics simulations, which indicated two conformations of the bound inhibitor, which involve cationic amino-acid side chains in the active-site region and residues around positions 15 and 116 located in the N- and C-termini respectively in the substrate recognition surface. These results were correlated with isothermal titration calorimetry data, which demonstrated 2.7 suramin-binding sites on the hsPLA2 gIIA. These results suggested that suramin represents a novel class of phospholipase A2 inhibitor

Mais de 95% de luz ultravioleta (UV) que atinge a superfície da Terra corresponde ao comprimento de onda da luz UVA (315-400 nm). A luz UVA induz no DNA danos pela absorção direta e indireta dos fótons, bem como por intermédio de cromóforos. Pacientes com Xeroderma Pigmentosum Variante (XP-V) possuem mutações na DNA polimerase &eta; (pol eta), que promove a síntese translesão dos danos induzidos pela luz solar. Na ausência dessa polimerase há aumento da mutagênese, provável causa de câncer de pele em pacientes XP-V. O objetivo deste trabalho foi caracterizar os mecanismos de indução de danos no genoma e mutagênese por luz UVA, em células derivadas desses pacientes. Os resultados indicam que a exposição à luz UVA resultou em maior sensibilidade de células XP-V comparadas à linhagem controle. Os níveis de fosforilação da histona H2AX (gerando &gamma;H2AX - indicador de indução de danos no genoma) e detecção de danos diretos e indiretos no DNA apresentou um aumento significativo em células XP-V irradiadas com luz UVA. Curiosamente, na ausência de pol eta houve uma redução na capacidade de remoção das lesões formadas. Além disso, a irradiação com luz UVA causou forte bloqueio de replicação do DNA e parada do ciclo celular em fase S em células XP-V, desencadeando importantes respostas mediadas por ATR/Chk1. Surpreendentemente, o antioxidante N-acetilcisteína (NAC) resultou em diminuição da sensibilidade celular, dos níveis de &gamma;H2AX, da parada de forquilha de replicação e do ciclo celular, reduziu os efeitos citotóxicos da inibição de ATR, melhorou o reparo de lesões no DNA e preveniu a carbonilação de proteínas em células XP-V irradiadas com luz UVA. Investigamos também a indução de mutagênese nas células irradiadas com luz UVA, através de sequenciamento de exoma de clones celulares. Os dados indicaram um aumento significativo da mutagênese em células XP-V irradiadas comparadas a células controle, e pela avaliação dos tipos de mutações encontradas verificamos uma frequência bastante alta de transições C>T, provavelmente como consequência de replicação errônea de dímeros de pirimidina. Entretanto, também identificamos indução significativa de transversões C>A, provavelmente devido a lesões oxidadas no genoma. Curiosamente, ao compararmos células XP-V com células controle detectamos um aumento desse último tipo de mutação na ausência de pol eta, provavelmente devido a lesões endógenas, produzidas pela oxidação do DNA. Além disso, análises in silico mostraram que células XP-V irradiadas com UVA apresentaram assinatura mutacional similar ao observado para tumores de pele. Os dados claramente indicam que células XP-V são sensíveis a irradiação com UVA e que os danos promovidos no DNA, incluindo aqueles causados por estresse oxidativo, desencadeiam respostas celulares e mutagênese nesses pacientes. Assim, além de apontar que UVA pode gerar efeitos deletérios na pele de pacientes XP-V, nossos dados também contribuem para a compreensão de como esses comprimentos de onda podem atuar em células humanas em geral / More than 95% of ultraviolet-light (UV) that reaches the Earth surface corresponds to UVA wavelengths (315-400 nm). UVA-light induces DNA damage through direct and indirect absorption of photons, as well as, intermediated by chromophores and by oxidation mechanisms. Xeroderma Pigmentosum Variant (XP-V) patients are defective in DNA polymerase &eta; (pol eta) that performs translesion synthesis of sunlight induced DNA damage. Absence of pol eta results in increased mutagenesis, which is probably responsible for high frequency of skin cancer in XP-V patients. The goal of this work was to characterize the mechanisms of UVA-induced genome DNA damage and mutagenesis in cells derived from these patients. The results indicate that UVA irradiation increased cell death of XP-V compared to control cell line. The phosphorylation of the histone H2AX (generating &gamma;H2AX, an indicator of genotoxic stress) and DNA damage was highly increased in UVA irradiated XP-V cells. Curiously, however, in the absence of pol eta, there was a reduction in the capacity of cells to remove DNA damage from genome. Moreover, UVA irradiation triggered strong DNA synthesis blockage and cell cycle arrest in S phase, resulting in important responses mediated by the ATR/Chk1 pathway in XP-V cells. Interestingly, the antioxidant N-acetyl cysteine (NAC) resulted in decreased cell sensitivity, &gamma;H2AX levels, fork stalling and cell cycle arrest, reduced the cytotoxic effect of ATR inhibition, improved DNA repair and prevented the protein carbonylation in XP-V cells irradiated with UVA. The mutagenesis by UVA-light was also investigated by exome DNA sequencing of cellular clones. The data indicated a significative increase of mutagenesis in XP-V irradiated cells compared to control cells, and the identification of mutation types indicated a high increase of C>T transitions, probably as result of error-prone replication of pyrimidine dimers. Nevertheless, the induction of C>A transversions were also detected, probably due to oxidized DNA damage. Curiously, when XP-V and control cells were compared, in the absence of irradiation, these transversions were also detected, maybe due to endogenous oxidation of DNA. In addition, in silico analyses showed that UVA-irradiated XP-V cells had a mutation signature similar to the observed for skin cancer. The data demonstrate XP-V cells are sensitive to UVA-light and DNA damage, including by oxidative stress, trigger cell responses and induce mutagenesis in these patients. Therefore, besides showing that UVA-irradiation may generate deleterious effects in the skin of XP-V patients, the data also contribute to understand how these light wavelengths may damage human cells in general

Lipoxygenasen sind nichthämeisenhaltige Dioxygenasen, die die Bildung von Hydroperoxiden aus molekularem Sauerstoff und mehrfach ungesättigten Fettsäuren katalysieren. Im Rahmen dieser Arbeit wurden verschiedene Lipoxygenase-Ligand-Wechselwirkungen untersucht: a) Durch gezielte Substratveränderungen und ortsgerichtete Mutagenese konnte gezeigt werden, dass Fettsäuren normalerweise mit dem Methylende in der Bindungstasche tierischer Lipoxygenasen gebunden werden. Unterschiedliche Positionsspezifitäten basieren demzufolge auf dem Volumen der Substratbindungstasche (Volumenhypothese). Darüber hinaus konnte bei der 15-Lipoxygenase eine inverse Substratbindung (Carboxylgruppe im aktiven Zentrum) durch Modifikation beider Enden der Fettsäure erzwungen werden, wodurch ausschließlich 5-Lipoxygenierung katalysiert wurde. b) Untersuchungen mit dem Hemmstoff Ebselen ergaben unterschiedliche Hemmmechanismen für verschiedene Enzymzustände. Die Hemmung der Lipoxygenase im Grundzustand (Fe[II]) erfolgt durch kovalente Bindung und Veränderung der Eisenligandensphäre irreversibel nach einem nicht-kompetitiven Mechanismus. Dagegen wird die aktive Lipoxygenase (Fe[III]) nur noch kompetitiv durch Ebselen gehemmt. c) Die Membranbindung der tierischen 15-Lipoxygenase erfolgt über hydrophobe Wechselwirkungen, vermittelt durch oberflächenexponierte, hydrophobe Aminosäuren aus beiden Enzymdomänen. Die Expression einer enzymatisch aktiven Trunkationsmutante, der die N-terminale Domäne fehlt, zeigte, dass diese nicht essentiell ist für die Membranbindung. / Lipoxygenases are nonheme iron-containig dioxygenases that catalyze the oxygenation of polyunsaturated fatty acids to hydroperoxy derivatives. Here, the interaction of lipoxygenases with various ligands was investigated: a) From substrate modifications and site directed mutagenesis it was concluded that fatty acids are bound with their methyl end in the substrate binding pocket of mammalian lipoxygenases. The positional specificity is therefore related to different volumes of this binding pocket (space-based hypothesis). For the 15-lipoxygenase an inverse substrate binding (carboxy terminus in the pocket) could be forced by simultaneous modification of both ends of the fatty acid. This lead to an exclusive 5-lipoxygenation by the 15-lipoxygenase. b) The mechanism of lipoxygenase inhibition by ebselen depends on the enzyme's state. The groundstate lipoxygenase (containing Fe[II]) is irreversibly inhibited in a non-competetive manner due to covalent modification and alteration of the iron ligand sphere. The active enzyme (containing Fe[III]) on the other hand is only competetively inhibited. c) The membrane binding of the mammalian 15-lipoxygenase is based on hydrophobic interactions mediated by solvent exposed, hydrophobic amino acid residues of both enzyme domains. The expression of an enzymatically active truncation mutant, which lacks the entire N-terminal domain, showed that this domain is not essential for membrane binding.

O sistema SOS controla a expressão de diversos genes, muitos envolvidos com o reparo de DNA. Caulobacter crescentus vem emergindo como um modelo alternativo interessante para o estudo de mecanismos de reparo de DNA. Temos como objetivos realizar uma análise funcional de genes de função desconhecida regulados por SOS, e investigar a indução de SOS por antibióticos beta-lactâmicos em C. crescentus. Análises funcionais dos genes CC_3424 e CC_3467 mostraram que deleções nestes genes resultam em fenótipo de sensibilidade à mitomicina C (MMC). CC_3424 possui similaridade com glioxalases e CC_3467 com endonucleases. Acreditamos que CC_3467 atue no reparo de ligações intercadeia no DNA, e que CC_3424 atue detoxificando a MMC das células. Estudos dos efeitos biológicos da indução do sistema SOS mostram que a cefalexina (CFE) induz este regulon em concentrações subinibitórias. Células tratadas com CFE apresentam mais danos oxidativos do tipo 8-oxoguanina. Estes resultados mostram que concentrações subinibitórias de CFE resultam em estresse oxidativo em C. crescentus. / The SOS response controls the expression of several genes, many of which are involved in DNA repair mechanisms. Caulobacter crescentus has emerged as an alternative bacterial model for DNA repair. As aims, we will undertake a functional analysis of some of the genes regulated by the SOS response, and will investigate the SOS induction by beta-lactam antibiotics in C. crescentus. Functional analysis of the genes CC_3424 and CC_3467 showed that deletions in these genes result in a phenotype of sensitivity to mitomycin C (MMC). CC_3424 has similarity to glyoxalase and CC_3467 to endonucleases. We believe that the CC_3467 gene plays a role in the repair of interstrand crosslinks in the DNA, while CC_3424 acts in MMC cellular detoxification. Studies of biological effects of SOS induction showed that subinibitory concentrations of cephalexin (CFE) induce the SOS regulon. Cells treated with CFE have higher concentrations of 8-oxoG oxidative damage. These results show that subinibitory concentrations of cephalexin leads to cellular oxidative stress in C. crescentus.

Escherichia coli patogênicas extraintestinais (ExPEC) causam colibacilose aviária, infecções do trato urinário e meningite neonatal em humanos. A cepa ExPEC MT78 é virulenta in vitro e in vivo, e possui a habilidade de invadir células eucarióticas. Para melhor entender o fenótipo invasivo dessa cepa, foi criada uma biblioteca de mutantes aleatórios pela técnica de mutagênese marcada com assinatura, e os mutantes foram selecionados negativamente em ensaio de invasão a fibroblastos aviários. Mutantes atenuados apresentaram mutação em genes do operon da fímbria do tipo 1 e nos genes de metabolismo de açúcares treA e bglB. Foram feitos mutantes específicos para o gene que codifica a enzima trealase periplasmática (TreA) e para o operon de metabolismo de β-glicosídeos (bgl). O mutante MT78ΔtreA apresentou, frente à cepa selvagem, diminuição na capacidade de adesão e invasão a fibroblastos aviários, na expressão da fímbria do tipo 1 e na capacidade de colonizar a bexiga de camundongos em modelo de infecção urinária. O mutante MT78Δbgl também apresentou, frente à cepa selvagem, diminuição na capacidade de adesão e invasão a fibroblastos aviários e na capacidade de colonizar a bexiga de camundongos em modelo de infecção urinária, mas não mostrou alteração na expressão da fímbria do tipo 1, medida por aglutinação de leveduras. Os resultados deste trabalho mostraram que a trealase periplasmática afeta a expressão da fímbria do tipo 1 e a virulência in vivo da cepa ExPEC MT78, enquanto o operon do metabolismo de β-glicosídeos afeta a virulência in vivo da cepa ExPEC MT78 por um mecanismo ainda não-elucidado. / Extraintestinal pathogenic E. coli (ExPEC) cause colibacillosis in birds, urinary tract infections and neonatal meningitis in humans. The ExPEC strain MT78 is virulent in vitro and in vivo, and is able to invade eukaryotic cells. In order to better understand the invasive phenotype of this strain, a library of random mutants was made using the signature-tagged mutagenesis approach. The mutants were negatively selected in invasion assays of avian fibroblasts. Attenuated mutants presented mutation in the type 1 fimbria operon and in the genes of sugar metabolism treA and bglB. Specific mutants were created for the periplasmic trehalase (TreA) gene and for the β-glycosides metabolism operon (bgl). The MT78ΔtreA mutant displayed, in comparison with the wild type strain, a reduction on the capacity of adhesion and invasion to avian fibroblastos, on type 1 fimbriae expression and on the capacity to colonize the bladder in a murine model of urinary tract infection. The MT78Δbgl mutant, compared to the wild type strain, also displayed a reduction on the capacity of adhesion and invasion to avian fibroblastos and on the capacity to colonize the bladder in a murine model of urinary tract infection, but did not show any difference on type 1 fimbriae expression as detected by yeast agglutination. Taken together, our results show that the periplasmic trehalase affects type 1 expression and in vivo virulence of the ExPEC strain MT78, and the operon for β-glycosides metabolism affects in vivo virulence by an as yet unidentified mechanism.

Coenzima Q (CoQ) é uma molécula de função essencial na transferência de elétrons da cadeia respiratória mitocondrial. Em Saccharomyces cerevisiae , a CoQ é constituída por um anel de benzeno associado a uma cadeia poliprenil, com 6 unidades de repetição, sendo por isso também denominada CoQ6 ou Q6. Ao todo já foram identificados treze genes (COQ1 COQ11, ARH1 e YAH1) nucleares necessários para biossíntese da CoQ. A maioria dos produtos Coq estão fisicamente associados em um complexo biossintético ancorado na membrana mitocondrial interna. Neste projeto, tentamos descrever resíduos relevantes de Coq3p e Coq7p aliando análises de bioinformática com testes fenotípicos para balizamento funcional. Coq7p é uma proteína com dois centros de ferro com íons carboxilato e catalisa a hidroxilação de demetoxi-Q6 (DMQ6). Neste estudo, indicamos um grupo de resíduos que modulam a atividade e a estabilidade de Coq7p: D53, R57, V111 e S114. Enquanto R57, V111 e S114 são resíduos muito conservados, V111 e S114 estão correlacionados em comunidades de coevolução. Aqui, demonstramos também que o duplo mutante S114A, V111G e o mutante S114E apresentam deficiência respiratória em temperatura não permissiva, além de acumularem o intermediário DMQ6 e sintetizarem baixas quantidades de Q6, concluindo assim que o fosmimético S114E inibe a atividade Coq7p. Dessa forma, propomos que a fosforilação do resíduo S114 promove o deslocamento de uma alça entre as hélices 2 e 3, afetando assim a atividade do centro catalítico Coq7p. Por sua vez, Coq3p atua como uma metiltransferase, catalisando diferentes passos durante a biossíntese da CoQ. Aqui, identificamos resíduos que colaboram para a atividade funcional de Coq3p: E123, S125, C131, G133, G134, H165, D203, E219, K258 e S262. Mutantes carregando as alterações E123A, H165A, D203A, E219A, K258A e S62A apresentam discreto crescimento respiratório e expressão de Coq3p similares à da linhagem selvagem, além de acumularem baixas quantidades de Q6. Enquanto C131, G133 e G134 são resíduos altamente conservados, localizados em uma alça no espaço entre fitas beta, no provável sítio ativo da proteína, mutantes C131A, G133A e G134A se superexpressos apresentam crescimento respiratório em meio contendo fonte de carbono não fermentável, além de acumularem Q6 compatíveis com os níveis de expressão proteica. Propomos assim um modelo para Coq3p, tendo os resíduos C131, G133 e G134 como centro catalítico de Coq3p. / Coenzyme Q (CoQ) is a molecule of essential function in the transfer of electrons of the mitochondrial respiratory chain. In saccharomyces cerevisiae , CoQ is constituted by a benzene ring associated with a polyprenyl chain with 6 repetition units, being therefore also denominated CoQ6 or Q6. Thirteen nuclear genes have already been identified (COQ1 COQ11, ARH1 and YAH1) required for coenzyme Q biosynthesis. Most of Coq products are physically associated in a biosynthetic complex anchored at the mitochondrial internal membrane. In this project, we identified Coq3p and Coq7p residues relevant for their respective role in CoQ synthesis combining bioinformatics analyzes with phenotypic tests for functional mapping. Coq7p is a carboxylate-bridged di-iron protein that catalyzes the hydroxylation of demetoxy-Q6 (DMQ6), the last monooxygenase step in the synthesis of CoQ. In this study, we found a group of residues that modulate the activity and stability of Coq7p: D53, R57, V111 and S114. While R57, V111 and S114 are highly conserved residues, V111 and S114 are correlated in communities of coevolution. We also demonstrate that the double mutant S114A, V111G and the mutant S114E have respiratory deficiency at non-permissive temperature, in addition to accumulating of the intermediate DMQ6 and low amounts of Q6, thus concluding that phosmimetic S114E inhibits the activity of Coq7p. Hence, we propose that the phosphorylation of S114 is required to move a loop between helices 2 and 3, thus affecting the activity of the catalytic center Coq7p. For its part, Coq3p acts as a methyltransferase, catalyzing different steps during biosynthesis of CoQ. Here we identified residues that collaborate for functional activity of Coq3p: E123, S125, C131, G133, G134, H165, D203, E219, K258 and S262. Mutants E123A, H165A, D203A, E219A, K258A and S62A, have mild respiratory growth, and expression of Coq3p levels similar to the wild strain, in addition to accumulating low amounts of Q6. While C131, G133, and G134 are residues highly conserved, located in a loop in the space between beta sheets, the overexpression of the mutants C131A, G133A and G134A present respiratory growth in medium containing non-fermentable carbon source, in addition to accumulate Q6 compatible with the levels of protein expression. We propose a model for Coq3p, with residues C131, G133 and G134 as part of Coq3p catalytic center.