This dissertation is a compilation of published work and a manuscript that seeks to understand the role of polyamine metabolism in the regulation of pneumococcal physiology. Streptococcus pneumoniae (pneumococcus) is the major cause of community-acquired pneumonia, and otitis media worldwide. Genetic diversity and serotype replacement, and antibiotics resistance to confound existing therapeutic strategies and limit the effectiveness of the available capsule polysaccharide (CPS) based vaccines. Polyamines such as putrescine, spermidine and cadaverine are ubiquitous polycationic hydrocarbons that interact with negatively charged molecules and modulate important cellular processes. Intracellular polyamine concentrations are regulated by biosynthesis, degradation, and transport. This work investigated the impact of the deletion of polyamine biosynthesis gene, SP_0916 (cadA, lysine/arginine decarboxylase covered in the second, third and fourth chapters), on growth, Gram staining characteristics, capsule production, proteome and stress responses of virulent pneumococcal serotype 4 (TIGR4). We identified loss of capsular polysaccharide (CPS) in DELTA SP_0916 strain. Our proteome results showed a shift in metabolism towards the pentose phosphate pathway (PPP) that could reduce the availability of precursors for CPS and could explain the un-encapsulated phenotype of DELTA SP_0916. Since a shift towards the PPP is usually in response to stress, we compared the stress responses of DELTA SP_0916 to that of TIGR4. Our results show that the mutant was more susceptible to oxidative, nitrosative, and acid stress compared to the wild type. In the fifth chapter we compared the transcriptome, metabolome, stress responses and stress susceptibility of the polyamine transport deficient strain (DELTA potABCD) and S. pneumoniae TIGR4. Results in this chapter show that polyamine transport is essential for pneumococcal stress responses, and capsule biosynthesis. The impact of impaired polyamine synthesis (DELTA SP_0916), and transport (DELTA potABCD) on pneumococcal capsule is due to altered expression of Leloir pathway, reduced glycolysis, and increased PPP, possibly in response to impaired stress responses. These results demonstrate that alteration of polyamine pathways affects pneumococcal stress responses which in turn could limit the availability of precursors for capsule synthesis, and thus have an impact on virulence. Thus, polyamine metabolism is an attractive avenue for developing novel interventions for limiting the spread of S. pneumoniae, a versatile human pathogen.

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京都大学 / 新制・課程博士 / 博士(農学) / 甲第24668号 / 農博第2551号 / 新制||農||1099(附属図書館) / 学位論文||R5||N5449(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 小川 順, 教授 栗原 達夫, 教授 伊福 健太郎 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

In Escherichia coli, the speC gene encodes biosynthetic ornithine decarboxylase (ODC), an enzyme that catalyzes the decarboxylation of ornithine to produce putrescine. The two polyamines, putrescine and spermidine, and the cyclic AMP (CAMP) - cAMP receptor protein (CRP) are known to inhibit the expression of ODC via undefined mechanisms. A single copy of the speC’-lacZ fusion plasmid pOL-1, containing an 843 base pair fragment including the spec promoter, was transferred to the E. coli CB806 chromosome to create E. coli λCBOL. In cell-free extracts prepared from E. coli λCBOL supplemented with cAMP, putrescine, or spermidine, the B-galactosidase activity encoded by the speC’-lacZ fusion was compared to the ODC activity encoded by spec. Only cyclic AMP and putrescine repressed the speC’-lacZ fusion. Cyclic AMP, putrescine, and spermidine all repressed the spec gene. A 444 bp AluI restriction fragment, containing a putative CRP binding site and a downstream open reading frame (ORF2) present on the strand complementary to speC, was fused to lacZ to create a transcriptional fusion, pCC2L. Analysis of E. coli CB806/pCC2L revealed that there was no detectable β8- galactosidase activity from the ORF2-lacZ fusion. However, promoter activity was detected in the opposite direction (3’ to 5’) of ORF2 as alkaline phosphatase activity, encoded on the same plasmid, increased in the presence of CAMP. A 678 bp DraI-AatII fragment, containing the CRP binding site and an adjacent open reading frame (ORF3) present on the speC coding strand, was subcloned into plasmid pBR322 to create pBCR. In the presence of 10 mM cAMP, E. coli CB806/pBCR exhibited an 18% inhibition in ODC activity encoded by spec. It is proposed that ORF3 encodes a protein that represses speC in the presence of CAMP. / Master of Science

In insects, the cuticle provides protection against physical injury and water loss, rigidness for muscle attachment and mechanical support, and flexibility in inter-segmental and joint areas for mobility. As most insects undergo metamorphosis, they need to shred off old cuticle and synthesize new cuticle to fit the body shape and size throughout their life cycles. The newly formed cuticle, mainly composed of cuticular proteins, chitin, and sclerotizing reagents, needs to be hardened through the crosslinks between cuticular proteins and sclerotizing reagents. This dissertation concerns the biochemical activities of several pyridoxal 5-phosphate (PLP)-dependent decarboxylases with most of them involved in insect cuticle hardening. Herein, we first present a detailed overview of topics in reactions and enzymes involved in insect cuticle hardening. Aspartate 1-decarboxylase (ADC) is at the center of this dissertation. beta-alanine, the product of ADC-catalyzed reaction from aspartate, is the component of an important sclerotizing reagent, N-beta-alanyldopamine; the levels of beta-alanine in insects regulate the concentrations of dopamine, therefore affecting insect sclerotization and tanning (collectively referred as cuticle hardening in this dissertation). Biochemical characterization of insect ADC has revealed that this enzyme has typical mammalian cysteine sulfinic acid decarboxylase (CSADC) activity, able to generate hypotaurine and taurine. The result throws lights on research in the physiological roles of insect ADC and the pathway of insect taurine biosynthesis. Cysteine was found to be  an inactivator of several PLP-dependent decarboxylases, such as ADC, glutamate decarboxylase (GAD) and CSADC. This study helps to understand symptoms associated with the abnormal cysteine concentrations in several neurodegenerative diseases. A mammalian enzyme, glutamate decarboxylase like-1 (GADL1), has been shown to have the same substrate usage as insect ADC does, potentially contributing to the biosynthesis of taurine and/or beta-alanine in mammalian species. Finally, the metabolic engineering work of L-3, 4-dihydroxyphenylalanine decarboxylase (DDC) and 3, 4-dihydroxylphenylacetaldehyde (DHPAA) synthase has revealed that the reactions of these enzymes could be determined by a few conserved residues at their active site. As both enzymes have been implicated in the biosynthesis of sclerotizing reagents, it is of great scientific and practical importance to understand the similarity and difference in their reaction mechanisms. The results of this dissertation provide valuable biochemical information of ADC, DDC, DHPAA synthase, and GADL1, all of which are PLP-dependent decarboxylases. ADC, DDC, DHPAA synthase are important enzymes in insect cuticle hardening by contributing to the biosynthesis of sclerotizing reagents. Knowledge towards understanding of these enzymes will promote the comprehension of insect cuticle hardening and help scientists to search for ideal insecticide targets. The characterization of GADL1 lays groundwork for future research of its potential role in taurine and beta-alanine metabolism. / Ph. D.

L'étude qu'on a entreprise a pour but d'analyser les facteurs de virulence des espèces "Classiques" et "nouvelles" de Brucella. Dans cette perspective, on a analysé les génomes des espèces récemment découvertes : Brucella inopinata BO1 et Brucella inopinata-like BO2, isolés pour la première fois de patients humains sans réservoir animal connu. On a découvert que ces deux espèces possèdent des profils de restriction uniques. De plus, BO2 possède deux chromosomes de taille identique, un profil jamais décrit pour une autre espèce de Brucella. L'analyse de la réplication intracellulaire de ces deux espèces révèle que BO2 ne se réplique pas dans les macrophages humains et murins alors que BO1 se réplique d'une façon similaire à Brucella suis 1330, ce qui confirme la potentielle implication de BO1 dans la pathogenèse chez l'homme. Sur un autre niveau d'analyse, on a été à la recherche de facteurs de virulence potentiels dans d'autres espèces de Brucella notamment Brucella microti et Brucella suis sur les niveaux génomique et post-transcriptionnel. Sur le niveau génomique, on a découvert que le système GAD (glutamate decarboxylase) confère une résistance à l'acidité à Brucella microti lors de son passage dans l'estomac. Sur le niveau post-transcriptionnel, on a isolé, séquencé et identifié les petits ARNs noncodant associés à la protéine chaperone Hfq, qui joue un rôle important dans la virulence de Brucella. / We have undertaken in this study a multidimensional analysis of the virulence factors of "Classical" and new "Brucella species". In this objective, we have analysed the genomes of newly described species Brucella inopinata BO1 and Brucella inopinata-like BO2 isolated for the first time from human patients with no known animal reservoir. We found that these two species have unique restriction profiles. In addition, BO2 has a unique chromosomal distribution with two chromosomes of the same size, never seen before in Brucella. Analysis of the intracellular replication of these strains reveals that BO2 is unable to replicate in neither human nor mouse macrophages while BO1 successfully entered and replicated as efficiently as Brucella suis 1330 confirming the potential virulence of this species for humans. On an other level of analysis, we looked for potential virulence factors in other Brucella species including Brucella microti and Brucella suis at the genomic and post-transcriptional level. At the genomic level we discovered that the glutamate decarboxylase system confers resistance to acidity to Brucella miroti during its transit in the stomach. On the post-transcriptional level, we isolated, sequenced and identified small noncoding RNAs associated to the chaperone protein Hfq, known to play a role in the virulence of Brucella.

Systemic lupus erythematosus (SLE) is the prototypic systemic autoimmune disease, whereas autoimmune polyendocrine syndrome type 1 (APS1) is a rare autosomal disorder characterized by combinations of organ-specific autoimmune manifestations including hypoparathyroidism and intestinal dysfunction, and may serve as a model for organ-specific autoimmunity. Autoantibodies directed against proteins expressed in the affected tissues are found in both diseases. From a chondrocyte cDNA expression library, we identified the protein AHNAK as an autoantigen in SLE. Anti-AHNAK antibodies were found in 29.5% (18/61) of patients with SLE, 4.6% (5/109) of patients with rheumatoid arthritis, and 1.2% (2/172) of blood donors. Using a candidate approach, we analyzed the prevalence in APS1 and other organ-specific autoimmune diseases, of autoantibodies against the pyridoxal phosphate-dependent enzymes histidine decarboxylase (HDC) and cysteine sulfinic acid decarboxylase (CSAD), which are structurally closely related to known autoantigens. Anti-HDC and anti-CSAD reactivity was detected exclusively in APS1 patient sera. Anti-HDC antibodies were detected in 37.1% (36/97) of the APS1 sera, did not cross-react with aromatic L-amino acid decarboxylase, and were associated with intestinal dysfunction and loss of histamine-producing gastric enterochromaffin-like cells. In contrast, anti-CSAD reactivity was detected in 3.6% (3/83) of APS1 sera and cross-reacted with recombinant glutamic acid decarboxylase. From a parathyroid cDNA expression library, novel spliced transcripts of the CLLD4 gene on human chromosome 13q14, encoding 26 and 31 kDa isoforms recognized by autoantibodies in 3.4% (3/87) of APS1 patients, were identified and found to be preferentially expressed in lung and ovary. Both isoforms contain an N-terminal BTB/POZ domain, similarly to the TNF-alpha-regulated protein B12, localize both to the cytoplasm and nucleus in transfected COS cells, and form oligomers in vitro. The CLLD4 gene is located in a region frequently deleted in several forms of cancer, including lung and ovarian tumors. In conclusion, we have identified and partially characterized AHNAK and HDC as two common targets of autoantibodies in SLE and APS1, respectively. We have also identified CSAD and CLLD4 as two minor autoantigens in APS1, one of which is a novel protein with unknown function.

α-Amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) and α-aminomuconate-ε-semialdehyde dehydrogenase (AMSDH) are two neighboring enzymes in the L-tryptophan and 2-nitrobenzoic acid degradation pathways. The substrates of the two enzymes, α-amino-β-carboxymuconate-ε-semialdehyde (ACMS) and α-aminomuconate-ε-semialdehyde (2-AMS), are unstable and spontaneously decay to quinolinic acid and picolinic acid, respectively. ACMSD utilizes a divalent zinc metal as cofactor and is a member of the amidohydrolase superfamily. In this dissertation work, we have identified an important histidine residue in the active site that plays dual roles in tuning metal selectivity and activating a metal bound water ligand using mutagenesis, resonance Raman, EPR, crystallography, and ICP metal analysis techniques. The crystal structures of ACMSD from Pseudomonas fluorescens (PfACMSD) have been solved as homodimers in our laboratory while human ACMSD (hACMSD) was annotated as a monomer by another group. To resolve this structural difference, we used two conserved active site arginine residues as probes to study the oligomeriztion state of ACMSD and demonstrated that these two arginine residues are involved in substrate binding and that both Pf- and h- ACMSD are catalytically active only in the dimeric state. Subsequently, we solved the crystal structure of hACMSD and found it to be a homodimer in both catalytically active and inhibitor-bound forms. AMSDH is an NAD+ dependent enzyme and belongs to the aldehyde dehydrogenase superfamily. Due to the high instability of its substrate, AMSDH has not been studied at the molecular level prior to our work. We have cloned and expressed PfAMSDH in E. coli. The purified protein has high activity towards both 2-AMS and 2-hydroxymuconate semialdehyde (2-HMS), a stable substrate analog. We have successfully crystallized AMSDH with/without NAD+ and solved the crystal structure at up to 1.95 Å resolution. Substrate bound ternary complex structures were obtained by soaking the NAD+ containing crystals with 2-AMS or 2-HMS. Notably, two covalently bound catalytic intermediates were captured and characterized using a combination of crystallography, stopped-flow, single crystal spectroscopy, and mass spectrometry. The first catalytic working model of AMSDH has been proposed based on our success in structural and spectroscopic characterization of the enzyme in five catalytically relevant states in this dissertation work.

O estresse de calor prejudica o crescimento e reprodução dos organismos vegetais, ao alterar a permeabilidade de membranas biológicas e desnaturar proteínas, limitando o metabolismo primário. Dentre as respostas ao estresse abiótico, está a síntese de metabólitos secundários. Braquicerina é um alcaloide monoterpeno indólico com ação antioxidante, protetora contra UV e antimutagênica sintetizado por partes aéreas de Psychotria brachyceras. O objetivo deste trabalho é investigar o metabolismo de braquicerina sob estresse de calor. Assim, espera-se contribuir para o conhecimento acerca do metabolismo secundário nas respostas ao estresse de calor, descrever a função in planta do composto, e fornecer ferramentas para obtenção do alcaloide para fins farmacêuticos. O acúmulo de braquicerina foi induzido em discos foliares mantidos a 40ºC por três dias, tanto em regime de elevação abrupta como gradual da temperatura. Baixa temperatura (10ºC) não afetou o acúmulo do alcaloide. Discos foliares de Psychotria carthagenensis, uma espécie que não sintetiza alcaloides monoterpeno indólicos, foram também desafiados por estresse de calor. Clorofila total, teor de peróxido de hidrogênio e peroxidação lipídica foram quantificados em ambas as espécies. P. carthagenensis foi relativamente tolerante ao calor, o que pode estar relacionado à sua elevada concentração de antocianinas, fortemente induzidas por choque térmico de 50ºC por 6h. Peroxidação lipídica foi reduzida nas amostras de P. brachyceras sob estresse de calor agudo ou gradual em comparação à condição controle, sendo este parâmetro inalterado nas duas condições em P. carthagenensis. O teor de peróxido de hidrogênio foi menor em P. brachyceras submetida a choque de térmico em relação ao controle, enquanto o mesmo parâmetro não foi alterado em P. carthagenensis. Discos foliares das espécies sensíveis ao calor Brugmansia suaveolens e Brassica oleracea, pré-tratadas com braquicerina em concentrações similares às encontradas em P. brachyceras, adquiriram fenótipo tolerante ao choque térmico. A expressão do gene que codifica a enzima triptofano descarboxilase (TDC), envolvida na biossíntese de braquicerina em P. brachyceras, foi fortemente inibida em discos foliares submetidos à 40ºC por 6h, 12h e 24h, sugerindo que o efeito da temperatura na estimulação de acúmulo de alcaloide ocorra em nível pós-transcricional. Em conjunto, os dados indicam que a exposição ao calor é um meio efetivo de aumentar o rendimento de braquicerina, cuja acumulação contribui para proteção contra os danos oxidativos associados. / Heat stress impairs plant growth and reproduction by altering membrane permeability and promoting protein denaturation, which limits primary metabolism. Secondary metabolites often take part in protection against abiotic stress responses. Brachycerine is a monoterpene indole alkaloid with antioxidant, UV protectant, and antimutagenic activity synthesized by Psychotria brachyceras shoots. Brachycerine metabolism was analyzed under heat stress, in order to shed light on brachycerine‘s in planta function and to provide potential tools to improve alkaloid yields for pharmaceutical analysis. Accumulation was induced in leaf disks kept at 40ºC for three days, both by abrupt and stepwise temperature increase. Brachycerine concentration was not affected by low temperature (10ºC) exposure. Leaf disks of Psychotria carthagenensis, a species devoided of alkaloids, were also challenged by heat. Total chlorophyll, hydrogen peroxide and lipid peroxidation concentrations were determined in both species. P. carthagenensis was relatively tolerant to heat treatments which may be explained by its high anthocyanin concentration, strongly induced by heat shock of 50ºC for 6h. Brugmansia suaveolens and Brassica oleracea, pre-treated with brachycerine in concentrations equivalent to those found in P. brachyceras, had a heat shock tolerant phenotype, based on chlorophyll content. Expression of the TRYPTOPHAN DECARBOXYLASE gene, which encodes for an enzyme involved in alkaloid biosynthesis (TDC) was strongly repressed in leaf disks exposed to 40ºC for 6h, 12h e 24h, suggesting that temperature effect may occur at post-transcriptional level. Taken together, data indicate that heat exposure is an effective means to increase yields of brachycerine, whose accumulation contributes to protect against associated oxidative damage.

R-phenylacetylcarbinol (PAC) is used as a precursor for production of ephedrine and pseudoephedrine, which are anti-asthmatics and nasal decongestants. PAC is produced from benzaldehyde and pyruvate mediated by pyruvate decarboxylase (PDC). A strain of Rhizopus javanicus was evaluated for its production of PDC. The morphology of R. javanicus was influenced by the degree of aeration/agitation. A relatively high specific PDC activity (328 U decarboxylase g-1 mycelium) was achieved when aeration/agitation were reduced significantly in the latter stages of cultivation. The stability of partially purified PDC and crude extract from R. javanicus were evaluated by examining the enzyme deactivation kinetic in various conditions. R. javanicus PDC was less stable than Candida utilis PDC currently used in our group. A kinetic model for the deactivation of partially purified PDC extracted from C. utilis by benzaldehyde (0?00 mM) in 2.5 M MOPS buffer has been developed. An initial lag period prior to deactivation was found to occur, with first order dependencies of PDC deactivation on exposure time and on benzaldehyde concentration. A mathematical model for the enzymatic biotransformation of PAC and its associated by-products has been developed using a schematic method devised by King and Altman (1956) for deriving the rate equations. The rate equations for substrates, product and by-products have been derived from the patterns for yeast PDC and combined with a deactivation model for PDC from C. utilis. Initial rate and biotransformation studies were applied to refine and validate a mathematical model for PAC production. The rate of PAC formation was directly proportional to the enzyme activity level up to 5.0 U carboligase ml-1. Michaelis-Menten kinetics were determined for the effect of pyruvate concentration on the reaction rate. The effect of benzaldehyde on the rate of PAC production followed the sigmoidal shape of the Monod-Wyman-Changeux (MWC) model. The biotransformation model, which also included a term for PDC inactivation by benzaldehyde, was used to determine the overall rate constants for the formation of PAC, acetaldehyde and acetoin. Implementation of digital pH control for PAC production in a well-stirred organic-aqueous two-phase biotransformation system with 20 mM MOPS and 2.5 M dipropylene glycol (DPG) in aqueous phase resulted in similar level of PAC production [1.01 M (151 g l-1) in an organic phase and 115 mM (17.2 g l-1) in an aqueous phase after 47 h] to the system with a more expensive 2.5 M MOPS buffer.