Polyamines are ubiquitous components of all living cells and their depletion usually causes growth arrest or cytostasis, a strategy employed for treatment of West-African trypanosomiasis. In the malaria parasite, Plasmodium falciparum, polyamine biosynthesis is regulated by the uniquely bifunctional protein, Sadenosylmethionine decarboxylase/ornithine decarboxylase (PfAdoMetDC/ODC). The unique nature of this protein could provide a selective mechanism for antimalarial treatment. To validate polyamine depletion and specifically PfAdoMetDC/ODC, as drug target for antimalarial therapeutic intervention, polyamine biosynthesis was completely restrained via the inhibition of both catalytic sites of PfAdoMetDC/ODC with DFMO and MDL73811. The physiological effects during the resulting cytostasis were studied with a comprehensive functional genomics approach. The study was preceded by various assays to determine the treatment dosage that would result in complete cytostasis, without non-specific chemical cytotoxicity. The results obtained revealed that the cytostatic mechanism with growth arrest of the treated parasites and normal progression of the untreated controls require special consideration for basic comparisons of response in terms of the assay methodology used and data analysis. This is particularly important when studying a multistage organism such as P. falciparum, which constantly develops and change during the intraerythrocytic developmental cycle, such that growth arrest compared to normal progression would result in significant differences merely due to stage. This critical principle was kept in mind throughout the investigation and was applied to the relative quantification of RNA, proteins and metabolites via a relative time zero approach as opposed to the standard parallel time point comparison. Three independent functional genomics investigations, namely transcriptomics, proteomics and metabolomics were conducted, in which highly synchronised 3D7 parasite cultures were treated during the schizont stage and parasites were sampled during a time course at three time points (just before and during cytostasis). Transcriptome analysis revealed the occurrence of a generalised transcriptional arrest just prior to the growth arrest. To our knowledge this is the first time that transcriptional arrest as the preceding mechanism of cytostasis due to polyamine depletion, was demonstrated. However, despite the transcriptional arrest, the abundance of 538 transcripts was differentially affected and included three perturbation-specific compensatory transcriptional responses: the increased abundance of the transcripts for lysine decarboxylase and ornithine aminotransferase (OAT) and the decreased abundance of that for S-adenosylmethionine synthetase (AdoMet synthetase). Pearson correlations indicated more subtle effects of the perturbation on the proteome and even more so on the metabolome where homeostasis was generally maintained, except downstream to the enzymatic blockade at PfAdoMetDC/ODC. The perturbation-specific compensatory roles of OAT in the regulation of ornithine and AdoMet synthetase in the regulation of AdoMet were confirmed on both the protein and metabolite levels, confirming their biological relevance. The results provide evidence that P. falciparum respond to alleviate the detrimental effects of polyamine depletion via the regulation of its transcriptome and subsequently the proteome and metabolome, which supports a role for transcriptional control in the regulation of polyamine and methionine metabolism within the parasite. The study concludes that polyamines are essential molecules for parasite survival and that PfAdoMetDC/ODC is a valid target for antimalarial drug development. / Thesis (PhD)--University of Pretoria, 2008. / Biochemistry / unrestricted

Les cotransporteurs cation-Cl (CCCs) appartiennent à une grande famille de protéines qui comprend neuf isoformes : CCCl à CCC7, qui permettent le mouvement du Cl" avec celui d'un Na+ et/ou K+ à travers la membrane cellulaire, CCC9, qui agit comme un transporteur de polyamine (PA) - glutamate, et CCC8, dont on en connaît pas la fonction. Les CCCs font aussi partie d'une famille plus large de protéines qui sont regroupées sous le nom de « amino acid - polyamine - orgcmocation carriers (APC) ». À l'exception de CCC9, cependant, les protéines impliquées dans le transport des PAs n'ont été isolées que chez les unicellulaires et ne font pas nécessairement partie de la famille des APC. Dans cette étude, nous avons trouvé que CCC8 joue vraisemblablement le rôle de transporteur de polyamines chez des espèces plus complexes puisque son expression dans les cellules HEK-293 augmente l'influx de spermidine à la surface cellulaire et puisque cette protéine est ubiquitaire chez les mammifères. Nous avons aussi observé que l'influx de spermidine dirigé par les cellules exprimant CCC8 est inhibé par la pentamidine, le methyl-glyoxal-bis-guanylhydrazone, le furosémide et la paraquat, et que cet influx est aussi associé avec celui certains ions comme le Na+ et le Cl". Ainsi, un groupe de substrats qui sont transportés par CCC8 a été découvert pour la première fois suite à ce travail tout comme l'identification d'un nouveau système de transport de polyamines dans les cellules animales. Ces résultats ont un intérêt majeur puisque les polyamines intracellulaires jouent un rôle clé dans la prolifération cellulaire.

Ornithine decarboxylase (ODC) catalyzes the decarboxylation of ornithine to produce the diamine, putrescine, in the bacterium Escherichia coli. The speC gene encoding ODC has been shown to be subject to transcriptional repression by either putrescine or the cAMP- cAMP receptor protein (CRP) complex. To determine whether these regulatory modes are independent, the expression of ODC was determined by measuring the specific activity of ODC in crude extracts prepared from exponentially grown cultures of wild type ~ coli K-12 as well as in strains unable to synthesize cAMP (cya) and/or CRP (crp). 1-5 mM cAMP repressed ODe activity 22-38% in wild type, 57-66% in the cya strain, and only 7-18% in the ~ strains. 2-10 mM putrescine repressed ODe activity 30-32% in wild type, 48-49% in the cya strain, and 37-38% in the ~ strain. As putrescine repressed ODe activity in the absence of eRP protein (i.e. in a crp strain), putrescine-mediated repression of ODe appears to be independent of the repression of ODC by the cAMP-eRP complex. This conclusion was verified by demonstrating th t .oDC repression by putrescine and cAMP together was additive. / Master of Science

In Escherichia coli, the speA gene encodes biosynthetic arginine decarboxylase (ADC), the first enzyme in a putrescine biosynthetic pathway. ADC converts arginine to agmatine, which is hydrolyzed by agmatine ureohydrolase, encoded by the speB gene, to putrescine and urea. ADC is negatively regulated by mechanisms requiring either cAMP and cAMP receptor protein (CRP) or putrescine. A 3,236 base pair (bp) BalI-AccI restriction fragment derived from plasmid pKA5, which contains a 7.5 kilobase (kb) E. coli genomic fragment in pBR322, was subcloned into pGEM-3Z to produce plasmids pRM15 and pRM59. Both pRM15 and pRM59 overexpress ADC and the DNA sequence of the BalI-AccI fragment in each plasmid was determined. A 2,119 bp restriction fragment containing 730 bp 5’ to speA, the speA promoter, and 1,389 bp (463 amino acids) of the 5’-end of speA was used to construct transcriptional (pRM161 and pRM162) and translational (pRM65) speA-lacZ fusion plasmids. The presence of the predicted 160,000 and 157,000 dalton ADC / Ph. D.

La lysine décarboxylase (LDC) appartient à une famille d'enzymes décamériques dépendantes du cofacteur PLP qui sont connus pour catalyser la réaction transformant la L-Lysine en cadavérine tout en consommant un proton. Dans les entérobactéries comme Escherichia coli, nous trouvons deux paralogues, LdcI et LdcC. LdcI permet de faire face à la bactérie au conditions hostile de pH acide lors du passage à travers du tract gastro-intestinale. LdcC est produite pendant la phase stationnaire et aussi quand les bactéries font face aux traitements antibiotiques. La cadavérine produite par les LDCs est connue pour protéger les bactéries du stress oxydant. Cela s’explique par le fait que la cadavérine bloque les porines de la membrane externe, réduisant ainsi la perméabilité des molécules responsables du stress acides et oxydant. L'activité des LDCs chez E. coli est coordonnée avec la réponse stringente qui est mise en place lorsque les microorganismes sont dans des conditions pauvres en nutriments, afin d’éviter l’épuisement intracellulaire de la L-Lysine nécessaire pour la synthèse des protéines. Cependant, cette inhibition peut être levée par la formation d'un complexe en forme de cage avec son partenaire RavA, permettant ainsi aux bactéries de faire face aux stress multiples. Etant donné que la réponse au stress est importante pour que les bactéries puissent exhiber leur pathogénicité, nous nous sommes demandés si la bactérie opportuniste Pseudomonas aeruginosa pourrait employer LdcA pour contrer des conditions de stress qui ont déjà été décrites pour LdcI chez les entérobactéries. Au cours de ma thèse, nous avons abordé cette question en utilisant différentes approches complémentaires. Tout d'abord, nous avons utilisé des fusions promoteur-gène et de l'analyse par Western-blot pour déterminer les conditions dans lesquelles le gène ldcA a été exprimé et sa protéine synthétisée. Nous avons pu observer que ldcA est exprimé sur la phase stationnaire de croissance dans des conditions aérobies en milieux riches et également pendant des conditions anaérobies de respiration avec nitrate. Nous avons également confirmé que l'expression de ldcA est régulée par ArgR et elle est induite complètement lorsque l’acide aminé L-arginine est présente dans le milieu de croissance. Même si nous avons trouvé que les conditions de stress n'induisent pas l'expression de ldcA, nous avons obtenu de nouvelles données suggérant que d'autres mécanismes de régulation tels que le système de quorum sensing dépendant des quinolones (PQS) pourraient être impliqués dans l'expression de ldcA. En utilisant des souches mutantes de ldcA et son complémentée, nous avons évalué si LdcA était impliqué dans la réponse au stress acide et oxydatif. Bien que les données obtenues à l'aide des expériences dans notre laboratoire et des technologies à haut débit (Biolog) aient révélé que LdcA ne présente pas les mêmes fonctions que LdcI, nous avons découvert que la cadavérine produite par LdcA est nécessaire pour la croissance en milieu minimal avec L- Glutamate comme source de carbone. Nous avons également examiné si la présence de LdcA modifie la résistance aux antibiotiques et nous montré que les rends moins persistants face aux carbenicillines. Enfin, en combinant l'analyse phylogénétique et structurelle, nous avons découvert que LdcA appartient à un sous-groupe différent de LDCs bactériennes. Les alignements de séquences montrent que les résidus clés nécessaires pour lier le ppGpp ne sont pas présents dans le site de liaison prédit ce qui a été confirmer par l'analyse biochimique. Notre travail montre que, malgré le fait que LdcA catalyse la même réaction enzymatique et partage les mêmes caractéristiques structurelles que LdcI et LdcC, elle ne joue pas le même rôle que ses homologues. Son rôle est lié aux effets physiologiques de la cadavérine et à la relation entre la L-lysine et le catabolisme de la L-arginine. / The lysine decarboxylase (LDC) belongs to a family of decameric PLP-dependent enzymes that catalyse the reaction transforming L-Lysine into cadaverine while consuming a proton. They are known to be involved in polyamine metabolism and during acid and oxidative stress responses.In enterobacteria like Escherichia coli, two paralogs are present, LdcI and LdcC. LdcI takes part in acid stress response by buffering bacterial cytoplasm. LdcC is produced during stationary phase and also when bacteria face fluoroquinolone treatment. The cadaverine produced by LDCs is known to scavenge reactive oxygen species (ROS) and is capable of blocking outer membrane proteins, thus reducing the permeability of molecules responsible for acid and oxidative stresses. The activity of the LDCs from E. coli is coordinated with the stringent response (nutrient starvation) in order to prevent intracellular L-Lysine depletion. The stringent response signal molecule ppGpp is able to bind directly to LDCs and inhibit their enzymatic activity. However, the inhibition of the LdcI can be prevented by the formation of a cage-like complex with its partner RavA allowing bacteria to face the challenge of both acid and nutrient stresses.Since mechanisms allowing bacteria to counter stress challenges are important for displaying full virulence, we wondered if the opportunistic bacterium Pseudomonas aeruginosa could be using LdcA to counter stress conditions that have already been described for LdcI in enterobacteria. During my PhD, we addressed this question by using different but complementary approaches.First of all, we used promoter-gene fusions and western-blot analysis to determine the conditions in which ldcA was expressed and its product synthesized. We could observe that ldcA is expressed on stationary phase under aerobic conditions in rich media and also during nitrate-respiring anaerobic conditions. As previously described in literature, we also confirmed that ldcA expression is regulated by ArgR and fully induced when L-Arginine is present in the growth medium. Even though we found out that acid and oxidative stress conditions do not induce the expression of ldcA, we obtained new data suggesting that other regulation mechanisms such as the quinolone signal system (PQS) could be involved in ldcA expression.In paralell, we constructed an ldcA mutant and its complemented strain to understand whether LdcA was involved in acid and oxidative stress response. Although the data obtained by using manual screenings and high-throughput technologies (Biolog) revealed that LdcA is not displaying the same functions as LdcI, we discovered that the cadaverine produced by LdcA is needed for full growth fitness when growing in minimal medium using L-glutamate as carbon source. Since slow growing phenotypes are linked to heightened bacterial persistence and because cadaverine has been shown to reduce the persisters population, we also examined if the presence of LdcA is modifying the amount of persisters during carbenicillin treatment. Our data has confirmed that this is indeed the case.Finally, by combining phylogenetic and structural analysis, we discovered that LdcA belongs to a different subgroup of bacterial LDCs. Sequence alignments show that key residues needed for binding ppGpp are not present in the predicted binding site which also suggests that the enzymatic activity is not inhibited by this molecule. And biochemical analysis has confirmed that this is indeed the case as it is the case for Arginine decarboxylases.Our work shows that, in spite of the fact that LdcA catalyses the same enzymatic reaction and shares the same structural fold than LdcI and LdcC, it is not implicated in acid stress or oxidative stress responses. Its role is linked to physiological effects of cadaverine and to the relationship between L-lysine and L-Arginine catabolism.

Abstract not available

Thesis (Ph. D.)--West Virginia University, 2001. / Title from document title page. Document formatted into pages; contains xiii, 165 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 157-165).

Putrescine, spermidine and spermine are the polyamines biosynthesized by human cells via ornithine decarboxylase (ODC) and are also sourced from the diet. Polyamines are required for malignant and normal cell growth and development. Pharmacological suppression of polyamine biosynthesis, by difluoromethylornithine, and inflammation, via sulindac, has demonstrated ~70% efficacy in preventing premalignant colorectal adenomas (CRA) in a clinical trial; however, high polyamine intakes mitigated this preventative action. Further, dietary polyamines increase the dysplasia of CRA in initiated animal models of colorectal cancer (CRC) and are hypothesized to function as tumor promoters. Human research on dietary polyamines was limited until the development of a dietary database in 2007 but, continues to be limited by the lack of a biomarker of exposure. Chapter 1 of this dissertation tests the hypothesis that dietary polyamines increase risk of CRA in polyp-formers (n = 1164) and found evidence to support this hypothesis. However, only women, younger participants and certain genotypes experienced more risk of CRA with high polyamine exposure. Chapter II tests the hypothesis that dietary polyamines increase the risk for CRC in an average risk cohort of post-menopausal women (n = 87,620) and did not find evidence to support this hypothesis in the whole population. Rather, dietary polyamines were non-significantly protective against CRC and significantly protective when paired with aspirin use and against CRC-specific death. There was some evidence to support an increase in risk of CRC in younger participants with high polyamine exposure. Overall, the first two chapters suggest that dietary polyamines protect the colorectum in normal risk individuals but promote carcinogenesis in high risk individuals. Chapter III tests the hypothesis that dietary polyamine intake correlates with urinary polyamine output in a group of overweight/obese, older men (n = 36) and Chapter IV tests the hypothesis that intake of highly ripe sweet cherries will increase urinary polyamine output in a subgroup of 10 men from Chapter III. The findings from these chapters suggest there may be a positive correlation, but that a better measure of dietary polyamine intake is needed to determine if urinary polyamines are biomarkers of exposure to polyamines.

Indiana University-Purdue University Indianapolis (IUPUI) / Pneumocystis pneumonia (PCP) is the leading opportunistic disease in immunocompromised individuals, particularly in AIDS patients. The alveolar macrophage (AM) is the major type of cell responsible for the clearance of Pneumocystis organisms; however, they undergo a high rate of apoptosis during PCP due to increased intracellular polyamine levels. This study examined the mechanism of this polyamine mediated apoptosis and investigated an alternative therapy for PCP by targeting this mechanism. The elevated polyamine levels were determined to be caused by increased polyamine synthesis and uptake. Increased polyamine uptake was found to be AM-specific, and recruited inflammatory cells including monocytes, B cells, and CD8+ T cells were found to be a potential source of polyamines. The expression of the antizyme inhibitor (AZI), which regulates both polyamine synthesis and uptake, was found to be greatly up-regulated in AMs during PCP. AZI overexpression was confirmed to be the cause of increased polyamine synthesis and uptake and apoptosis of AMs during PCP by gene knockdown assays. Pneumocystis organisms and zymosan were found to induce AZI overexpression in AMs, suggesting that the β-glucan of the Pneumocystis cell wall is responsible for this AZI up-regulation. In addition, levels of mRNA, protein, and activity of polyamine oxidase (PAO) were also found to be increased in AMs during PCP, and its substrates N1-acetylspermidine and N1-acetylspermine were found to induce its up-regulation. These results indicate that the H2O2 generated during PAO-mediated polyamine catabolism caused AMs to undergo apoptosis. Since increased polyamine uptake was demonstrated to be a pathogenic mechanism of PCP in this study, the potential therapeutic activity of five putative polyamine transport inhibitors against PCP was tested. Results showed that compound 44-Ant-44 significantly decreased pulmonary inflammation, organism burden, and macrophage apoptosis, and prolonged the survival of rats with PCP. In summary, this study demonstrated that Pneumocystis organisms induce AZI overexpression, leading to increased polyamine synthesis, uptake, and apoptosis rate in AMs and that targeting polyamine transport is a viable therapeutic approach against PCP.

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences