Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [114]-124).

Thesis (Ph. D.)--University of Washington, 1996. / Vita. Includes bibliographical references (leaves [135]-144).

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 186-200).

The activity of dihydrofolate reductase, a key enzyme in the de novo biosynthesis of thymidylate, purines, and some amino acids, had previously been found to be increased in a methotrexate-resistant mouse leukemia (L5178Y) cell line as compared to the activity in the parental methotrexate-sensitive cell line. The increased activity was composed of two forms of the enzyme, one of which, form 2, was highly insensitive to inhibition by methotrexate. Both forms were purified to near homogeneity and using the antibodies prepared against them, it could be demonstrated that the two forms are antigenically distinct. The increased dihydrofolate reductase activity present in the methotrexate resistant cells resulted from an overproduction of both forms of the enzyme due to the presence of abundant mRNA coding for these enzymes. An increase in the dihydrofolate reductase gene copy number could be demonstrated in the resistant cells. mRNA coding for form 1 and form 2 enzymes was greatly enriched by polysome immunoprecipitation and complimentary DNA (cDNA) was synthesized in vitro from these enriched mRNA molecules. Evidence was found for the presence of methotrexate-insensitive forms of dihydroflate reductase in the blast cells of three out of eight acute myelogenous leukemia patients, and in two (distinct from the above) of the eight patients the activity was significantly increased. In contrast to the overproduction of dihydrofolate reductase protein in the methotrexate-resistant mouse cell line, increased enzyme activity in a methotrexate-resistant human promyelocytic leukemia (HL-60) cell line could not be correlated with an increase in the enzyme protein. Furthermore, the amounts of dihydrofolate reductase mRNA and gene-dosages were similar in the parental metho-trexate-sensitive and methotrexate-resistant cells. The enzyme from the resistant cells differed significantly in some of its physical and kinetic properties from that present in the parental cells. An increase in dihydrofolate reductase activity resulting from a modification of the enzyme rather than gene amplification has not to date been reported in the literature and may present a novel mechanism of resistance to methotrexate. / Medicine, Faculty of / Pathology and Laboratory Medicine, Department of / Graduate

Thesis addresses the physiological role of formyl tetrahydrofolate synthetase (Fhs) and bifunctional folate dehydrogenase (FolD) in folate mediated one carbon metabolism in bacteria. Thesis consists of 5 chapters. First chapter provides the details of the literature on folate metabolism, enzymes involved the synthesis and physiological roles various folate co-factors. Second chapter discusses the study of Clostridium perfringens Fhs generation of folD deletion in the support of fhs. Third chapter explores the characterization of the folD deletion strain. Fourth chapter presents the characterization of monofunctional versions of FolD from Clostridium perfringens. Fifth chapters talks about anti-correlation existence of Fhs and PurT (phosphoribosyl glycinamide formyl transferase II) The detailed experimental study is discussed below i. Characterization of Clostridium perfringens Formyl Tetrahydrofolate Synthetase (Fhs) In this chapter we have characterized Fhs from pathogenic Clostridium perfringens. Fhs catalyzes the formation of N10-formyl THF from THF and formate. Previously Fhs has been characterized from various non-pathogenic species of Clostridium. In addition, the detailed kinetic parameters are not known. In this report we have characterized the Fhs Clostridium perfringens and detailed kinetic parameters were determined. We have also shown the biological function by rescue of UV photorepair sensitive strain. ii. One-carbon metabolic pathway rewiring in Escherichia coli reveals an evolutionary advantage of 10-formyltetrahydrofolate synthetase (Fhs) in survival under hypoxia In cells, N10-formyltetrahydrofolate (N10-formyl THF) required for formylation of eubacterial/organeller initiator tRNA and purine biosynthesis is produced by methylene- tetrahydrofolate dehydrogenase/cyclohydrolase (FolD) and/or 10-formyltetrahydrofolate synthetase (Fhs). folD is present in all organisms, where as fhs shows mixed distribution. We show that in E. coli, which naturally lacks fhs, essential function of folD could be replaced with fhs of Clostridium perfringens when provided on a medium copy plasmid or integrated as single copy gene in the chromosome of the ∆folD strains, for their growth in a complex medium. However, these strains require purines and glycine as supplements for growth in M9 minimal medium. The in vivo levels of N10-formyl THF in the ∆folD strains (harboring fhs) were limiting despite their high enzymatic capacity to synthesize the same. Auxotrophy for purines could be alleviated by adding formate to the medium, and that for glycine by engineering THF import into the cells. The ∆folD strains showed high NADP+/NADPH ratio and were hypersensitive to trimethoprim (TMP). Further, the presence of fhs was disadvantageous to E. coli under aerobic growth. However, under hypoxia, E. coli strains harboring fhs outcompeted those lacking it. And, the computational analysis revealed a predominant natural occurrence of fhs in anaerobic and facultative anaerobic bacteria. We also propose that inhibitors aimed at folD could potentiate the effect TMP drugs. iii. 5, 10-methylene-THF dehydrogenase (DH) and 5, 10-methenyl-THF cyclohydrolase (CH) activities of FolD are essential to maintain folate homeostasis and anti-folate resistance While E. coli and many other organisms have folD alone or folD and fhs, Clostridium species possess an annotated bi-functional FolD and an annotated methenyl tetrahydrofolate cyclohydrolase (FchA). Simultaneous presence of 3 enzymes for the synthesis of N10-formyl THF was intriguing. To understand this unusual feature we have cloned Clostridium perfringens CpeFolD and CpeFchA, over expressed and purified to near homogeneity. Biochemical analyses revealed that CpeFolD possess only dehydrogenase activity as opposed to in silico prediction, while CpeFchA possess cyclohydrolase activity as expected. We also show that expression of both proteins together allowed folD deletion in E. coli. From this study we found that presence of dehydrogenase and cyclohydrolase functions are very important in the maintenance of folate homeostasis and anti-folate resistance. iv. Analysis of distribution of fhs and purT genes in the organisms While analysing distribution of fhs across genomes, serendipitously we also found that large number of organism which have fhs lack purT(phosphoribosyl glycinamide formyl transferase II), in short where ever purT was present fhs was absent. This kind of anti-correlation was strictly conserved in Bacillus genes as well. Growth competition experiments were done to address anti-correlation between fhs and purT. Growth competition experiments revealed that simultaneous presence of both purT and fhs is disadvantageous, when compared to presence of either one gene.

Os defeitos de fechamento de tubo neural constituem uma das malformações mais freqüentes na espécie humana, apresentando alta morbi-mortalidade. Sua etiologia é considerada multifatorial, estando envolvidos fatores genéticos e ambientais. Estes fatores estão relacionados principalmente com o metabolismo da homocisteína. Realizamos um estudo de caso-controle com o objetivo de estudar os fatores bioquímicos e genéticos relacionados ao DTN na nossa população. Em pares de afetados com DTN e suas mães e pares de pacientes normais e suas mães foram avaliados dosagem de folato, vitamina B12, homocisteína e polimorfismos da enzima metileno tetraidrofolato redutase (MTHFR), C677T e A1298C. A dosagem de folato nos casos foi 11,37 ng/mL(±6,72) e nos controles 5,64 ng/mL(±4,16) (p<0,001). O folato sérico das mães foi 7,27 ng/mL (±4,48) e 3,90 ng/mL (±1,77) nas mães controles (p<0,001). A média de dosagem de vitamina B12 foi de 641,88 pg/mL ((±262,21) nos casos e 743,27 pg/mL (±433,52) nos controles (p= 0,205). A média de dosagem de vitamina B12 nas mães dos casos foi 354,75 pg/mL (±142,06) e 465,25 pg/mL (±194,91) nas mães controles (p=0,004). O nível de homocisteína plasmático médio foi 6,89 μmol/L(±4,48) para os casos e 5,41 μmol/L (±2,55) para os controles (p=0,099). Nas mães dos casos a dosagem média de homocisteína foi 7,23 μmol/L (±2,64) e 7,00 μmol/L (±2,24) nas mães controles (p=0,666). Não houve diferença entre a freqüência dos genótipos C677T e A1298C da MTHFR nos casos e controles e suas mães. Para o polimorfismo C677T as freqüências dos alelo C e T foram respectivamente 0,6585 e 0,3414 nos pacientes com DTN; 0,6590 e 0,3410 nos controles; 0,6460 e 0,3540 nas mães dos casos e 0,6136 e 0,3860 nas mães controles. Para o polimorfismo A1298C as freqüências dos alelos A e C foram respectivamente 0,7436 e 0,2564 nos pacientes com DTN; 0,7610 e 0,2390 nos controles; 0,8055 e 0,1945 nas mães dos casos e 0,8065 e 0,1935 nas mães controles. Identificamos que indivíduos homozigotos 677TT apresentam um maior nível de homocisteína e este é inversamente relacionado com os níveis de vitamina B12. Estes achados sugerem que uma alteração metabólica relacionada ao metabolismo da homocisteína e principalmente devido à diminuição da vitamina B12 seja um fator de risco para DTN na nossa população. / Neural tube defects (NTD) are among the most common birth defect leading to great disabilities. The etiology is multifactorial, involving the combined action of both genetic and environmental factors. Those factors have been related to homocysteine metabolism. We performed a case control study in order to evaluate the biochemical and genetic factors related to NTD in the South of Brazil. A mother- NTD children pair and mother normal children were evaluated for folate, vitamin B12, homocysteine and two polymorphism of the methylene tetrahydrofolate reductase (MTHFR), C677T and A1298C. The folate level was 11,37 ng/mL (±6,72) in the NTD patients and 5,64 ng/mL(±4,16) in the controls (p<0,001). The folate was 7,27 ng/mL (±4,48) in the NTD mothers and 3,90 ng/mL (±1,77) in the control mothers (p<0,001). The level of vitamin B12 was 641,88 pg/mL ((±262,21) in the NTD case and 743,27 pg/mL (±433,52) in the controls (p= 0,205). The levels of vitamin B12 in the NTD mothers was 354,75 pg/mL (±142,06) and 465,25 pg/mL (±194,91) in the control mothers (p=0,004). The pasmatic homocysteine level was 6,89 μmol/L(±4,48) for the NTD cases and 5,41 μmol/L (±2,55) for the controls (p=0,099). The NTD mothers showed homocysteine level of 7,23 μmol/L (±2,64) and the controls mothers demonstrated 7,00 μmol/L (±2,24) (p=0,666). We could not observed a difference between the frequency of the genotypes C677T and A1298C in case and controls. The frequency of the alele C and T for the polymorphism C677T were respectively 0,6585 and 0,3414 for the NTD patients; 0,6590 and 0,3410 for the controls; 0,6460 and 0,3540 for NTD mothers; 0,6136 and 0,3860 for the control mothers. The frequencies of the allele A and C for the polymorphism A1298C were respectively 0,7436 and 0,2564 for NTD patients, 0,7610 and 0,2390 for controls; 0,8055 and 0,1945 for NTD mothers; 0,8065 and 0,1935 for controls mothers. We could demonstrated that the homozygous 677TT had a higher level of homocysteine and this was related to low level of vitamin B12. Those findings suggest that biochemical and genetic factors related to homocysteine metabolism and vitamin B12 deficiency are a risk factor to NTD in our population.

Os defeitos de fechamento de tubo neural constituem uma das malformações mais freqüentes na espécie humana, apresentando alta morbi-mortalidade. Sua etiologia é considerada multifatorial, estando envolvidos fatores genéticos e ambientais. Estes fatores estão relacionados principalmente com o metabolismo da homocisteína. Realizamos um estudo de caso-controle com o objetivo de estudar os fatores bioquímicos e genéticos relacionados ao DTN na nossa população. Em pares de afetados com DTN e suas mães e pares de pacientes normais e suas mães foram avaliados dosagem de folato, vitamina B12, homocisteína e polimorfismos da enzima metileno tetraidrofolato redutase (MTHFR), C677T e A1298C. A dosagem de folato nos casos foi 11,37 ng/mL(±6,72) e nos controles 5,64 ng/mL(±4,16) (p<0,001). O folato sérico das mães foi 7,27 ng/mL (±4,48) e 3,90 ng/mL (±1,77) nas mães controles (p<0,001). A média de dosagem de vitamina B12 foi de 641,88 pg/mL ((±262,21) nos casos e 743,27 pg/mL (±433,52) nos controles (p= 0,205). A média de dosagem de vitamina B12 nas mães dos casos foi 354,75 pg/mL (±142,06) e 465,25 pg/mL (±194,91) nas mães controles (p=0,004). O nível de homocisteína plasmático médio foi 6,89 μmol/L(±4,48) para os casos e 5,41 μmol/L (±2,55) para os controles (p=0,099). Nas mães dos casos a dosagem média de homocisteína foi 7,23 μmol/L (±2,64) e 7,00 μmol/L (±2,24) nas mães controles (p=0,666). Não houve diferença entre a freqüência dos genótipos C677T e A1298C da MTHFR nos casos e controles e suas mães. Para o polimorfismo C677T as freqüências dos alelo C e T foram respectivamente 0,6585 e 0,3414 nos pacientes com DTN; 0,6590 e 0,3410 nos controles; 0,6460 e 0,3540 nas mães dos casos e 0,6136 e 0,3860 nas mães controles. Para o polimorfismo A1298C as freqüências dos alelos A e C foram respectivamente 0,7436 e 0,2564 nos pacientes com DTN; 0,7610 e 0,2390 nos controles; 0,8055 e 0,1945 nas mães dos casos e 0,8065 e 0,1935 nas mães controles. Identificamos que indivíduos homozigotos 677TT apresentam um maior nível de homocisteína e este é inversamente relacionado com os níveis de vitamina B12. Estes achados sugerem que uma alteração metabólica relacionada ao metabolismo da homocisteína e principalmente devido à diminuição da vitamina B12 seja um fator de risco para DTN na nossa população. / Neural tube defects (NTD) are among the most common birth defect leading to great disabilities. The etiology is multifactorial, involving the combined action of both genetic and environmental factors. Those factors have been related to homocysteine metabolism. We performed a case control study in order to evaluate the biochemical and genetic factors related to NTD in the South of Brazil. A mother- NTD children pair and mother normal children were evaluated for folate, vitamin B12, homocysteine and two polymorphism of the methylene tetrahydrofolate reductase (MTHFR), C677T and A1298C. The folate level was 11,37 ng/mL (±6,72) in the NTD patients and 5,64 ng/mL(±4,16) in the controls (p<0,001). The folate was 7,27 ng/mL (±4,48) in the NTD mothers and 3,90 ng/mL (±1,77) in the control mothers (p<0,001). The level of vitamin B12 was 641,88 pg/mL ((±262,21) in the NTD case and 743,27 pg/mL (±433,52) in the controls (p= 0,205). The levels of vitamin B12 in the NTD mothers was 354,75 pg/mL (±142,06) and 465,25 pg/mL (±194,91) in the control mothers (p=0,004). The pasmatic homocysteine level was 6,89 μmol/L(±4,48) for the NTD cases and 5,41 μmol/L (±2,55) for the controls (p=0,099). The NTD mothers showed homocysteine level of 7,23 μmol/L (±2,64) and the controls mothers demonstrated 7,00 μmol/L (±2,24) (p=0,666). We could not observed a difference between the frequency of the genotypes C677T and A1298C in case and controls. The frequency of the alele C and T for the polymorphism C677T were respectively 0,6585 and 0,3414 for the NTD patients; 0,6590 and 0,3410 for the controls; 0,6460 and 0,3540 for NTD mothers; 0,6136 and 0,3860 for the control mothers. The frequencies of the allele A and C for the polymorphism A1298C were respectively 0,7436 and 0,2564 for NTD patients, 0,7610 and 0,2390 for controls; 0,8055 and 0,1945 for NTD mothers; 0,8065 and 0,1935 for controls mothers. We could demonstrated that the homozygous 677TT had a higher level of homocysteine and this was related to low level of vitamin B12. Those findings suggest that biochemical and genetic factors related to homocysteine metabolism and vitamin B12 deficiency are a risk factor to NTD in our population.

Os defeitos de fechamento de tubo neural constituem uma das malformações mais freqüentes na espécie humana, apresentando alta morbi-mortalidade. Sua etiologia é considerada multifatorial, estando envolvidos fatores genéticos e ambientais. Estes fatores estão relacionados principalmente com o metabolismo da homocisteína. Realizamos um estudo de caso-controle com o objetivo de estudar os fatores bioquímicos e genéticos relacionados ao DTN na nossa população. Em pares de afetados com DTN e suas mães e pares de pacientes normais e suas mães foram avaliados dosagem de folato, vitamina B12, homocisteína e polimorfismos da enzima metileno tetraidrofolato redutase (MTHFR), C677T e A1298C. A dosagem de folato nos casos foi 11,37 ng/mL(±6,72) e nos controles 5,64 ng/mL(±4,16) (p<0,001). O folato sérico das mães foi 7,27 ng/mL (±4,48) e 3,90 ng/mL (±1,77) nas mães controles (p<0,001). A média de dosagem de vitamina B12 foi de 641,88 pg/mL ((±262,21) nos casos e 743,27 pg/mL (±433,52) nos controles (p= 0,205). A média de dosagem de vitamina B12 nas mães dos casos foi 354,75 pg/mL (±142,06) e 465,25 pg/mL (±194,91) nas mães controles (p=0,004). O nível de homocisteína plasmático médio foi 6,89 μmol/L(±4,48) para os casos e 5,41 μmol/L (±2,55) para os controles (p=0,099). Nas mães dos casos a dosagem média de homocisteína foi 7,23 μmol/L (±2,64) e 7,00 μmol/L (±2,24) nas mães controles (p=0,666). Não houve diferença entre a freqüência dos genótipos C677T e A1298C da MTHFR nos casos e controles e suas mães. Para o polimorfismo C677T as freqüências dos alelo C e T foram respectivamente 0,6585 e 0,3414 nos pacientes com DTN; 0,6590 e 0,3410 nos controles; 0,6460 e 0,3540 nas mães dos casos e 0,6136 e 0,3860 nas mães controles. Para o polimorfismo A1298C as freqüências dos alelos A e C foram respectivamente 0,7436 e 0,2564 nos pacientes com DTN; 0,7610 e 0,2390 nos controles; 0,8055 e 0,1945 nas mães dos casos e 0,8065 e 0,1935 nas mães controles. Identificamos que indivíduos homozigotos 677TT apresentam um maior nível de homocisteína e este é inversamente relacionado com os níveis de vitamina B12. Estes achados sugerem que uma alteração metabólica relacionada ao metabolismo da homocisteína e principalmente devido à diminuição da vitamina B12 seja um fator de risco para DTN na nossa população. / Neural tube defects (NTD) are among the most common birth defect leading to great disabilities. The etiology is multifactorial, involving the combined action of both genetic and environmental factors. Those factors have been related to homocysteine metabolism. We performed a case control study in order to evaluate the biochemical and genetic factors related to NTD in the South of Brazil. A mother- NTD children pair and mother normal children were evaluated for folate, vitamin B12, homocysteine and two polymorphism of the methylene tetrahydrofolate reductase (MTHFR), C677T and A1298C. The folate level was 11,37 ng/mL (±6,72) in the NTD patients and 5,64 ng/mL(±4,16) in the controls (p<0,001). The folate was 7,27 ng/mL (±4,48) in the NTD mothers and 3,90 ng/mL (±1,77) in the control mothers (p<0,001). The level of vitamin B12 was 641,88 pg/mL ((±262,21) in the NTD case and 743,27 pg/mL (±433,52) in the controls (p= 0,205). The levels of vitamin B12 in the NTD mothers was 354,75 pg/mL (±142,06) and 465,25 pg/mL (±194,91) in the control mothers (p=0,004). The pasmatic homocysteine level was 6,89 μmol/L(±4,48) for the NTD cases and 5,41 μmol/L (±2,55) for the controls (p=0,099). The NTD mothers showed homocysteine level of 7,23 μmol/L (±2,64) and the controls mothers demonstrated 7,00 μmol/L (±2,24) (p=0,666). We could not observed a difference between the frequency of the genotypes C677T and A1298C in case and controls. The frequency of the alele C and T for the polymorphism C677T were respectively 0,6585 and 0,3414 for the NTD patients; 0,6590 and 0,3410 for the controls; 0,6460 and 0,3540 for NTD mothers; 0,6136 and 0,3860 for the control mothers. The frequencies of the allele A and C for the polymorphism A1298C were respectively 0,7436 and 0,2564 for NTD patients, 0,7610 and 0,2390 for controls; 0,8055 and 0,1945 for NTD mothers; 0,8065 and 0,1935 for controls mothers. We could demonstrated that the homozygous 677TT had a higher level of homocysteine and this was related to low level of vitamin B12. Those findings suggest that biochemical and genetic factors related to homocysteine metabolism and vitamin B12 deficiency are a risk factor to NTD in our population.

Hydrogenasen sind komplexe Enzyme, die die reversible Oxidation von molekularem Wasserstoff zu Protonen und Elektronen katalysieren. Diese Enzyme erlauben ihrem Wirtsorganismus das Wachstum unter chemolithoautotrophen Bedingungen. Der Modellorganismus Ralstonia eutropha besitzt drei gut charakterisierte Hydrogenasen der [NiFe]-Klasse, die sich durch ihre Sauerstofftoleranz auszeichnen. Ihr aktives Zentrum besteht aus einer komplexen prosthetischen Gruppe, welche aus einem Nickel- und einem Eisenatom besteht. Letzteres koordiniert drei diatomare Liganden, zwei Cyanide und ein CO. Die Synthese der gesamten Ni(SR)2(µ-SR)2Fe(CN)2(CO)-Gruppe ist ein komplexer Prozess. Die sogenannte Maturation benötigt wenigstens sechs akzessorische Proteine, die sogenannten Hyp-Proteine. Das umfassende Verständnis dieser Maturationsprozesse ermöglicht eine Vielzahl von biotechnologischen Anwendungen. Die vorliegende Arbeit untersucht die Maturation unter verschiedenen Gesichtspunkten. Zentrale, offene Fragen sind die Herkunft des Carbonylliganden sowie die Prozesse, die zur Ligandierung des katalytischen Eisens führen. Dazu wurden molekularbiologische, biochemische und spektroskopische Methoden in Verbindung mit Isotopenmarkierung eingesetzt. Unter anderem konnte dabei gezeigt werden, dass das katalytische Eisen alle seine Liganden bereits im HypCD-Komplex, dem zentralen Element der Maturation, erhält. Ferner konnte in dieser Arbeit, erstmalig für [NiFe]-Hydrogenasen, eine konkrete Biosynthese des seltenen und toxischen diatomaren CO-Liganden beschrieben werden. Ausgehend vom Alpha-Kohlenstoff von Glycin wird der Tetrahydrofolat (THF)-abhängige C1-Metabolismus mit C1-Einheiten versorgt. Durch die enzymatische Aktivität von HypX wird die Formylgruppe von N10-Formyl-THF zu CO umgesetzt. / Hydrogenases are complex enzymes that catalyze the reversible oxidation of molecular hydrogen into protons and electrons. These enzymes allow their host organism to grow under chemolithoautotrophic conditions. The model organism Ralstonia eutropha has three well-characterized [NiFe]-hydrogenases, which exhibit an extraordinary high oxygen tolerance. Its active center is a complex prosthetic group which consists of a nickel and iron atom. The latter coordinates three diatomic ligands, two cyanides and one CO. The biosynthesis of the whole Ni(SR)2(μ-SR)2Fe(CN)2(CO)-group is a complex process. This so-called maturation process needs the activity of at least six accessory proteins, the Hyp-proteins. Understanding the maturation allows a variety of biotechnological applications. The present study examines the maturation of [NiFe]-hydrogenases under different aspects. The major questions concern the origin of the carbonyl ligand as well as the processes that lead to ligandation of the designated catalytic iron. To adress these tasks, molecular biological, biochemical and spectroscopic methods in combination with isotopic labeling were employed. Inter alia, it could be shown that the catalytic iron in the HypCD-complex, the central element of the maturation process, contains all three diatomic ligands. Furthermore, this study describes, for the first time in [NiFe]-hydrogenases, a specific biosynthetic route of the rare and toxic diatomic CO-ligand. Starting from the alpha-carbon of glycine the tetrahydrofolate (THF)-dependent one-carbon metabolism is replenished with one-carbon units. Subsequently the formyl group from N10-formyl-THF is hydrolyzed by the enzymatic activity from HypX and further converted to carbon monoxide as determined by isotopic labeling and infrared spectroscopy.