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Oomycetes, such as Phytophthora sojae, are plant pathogens that employ protein effectors that enter host cells to facilitate infection. Plants may overcome infection by recognizing pathogen effectors via intracellular receptors (R proteins) that form part of their defense system. Entry of some effector proteins into plant cells is mediated by conserved RxLR motifs in the effectors and phosphoinositides (PIPs) resident in the host plasma membrane such as phosphatidylinositol 3-phosphate (PtdIns(3)P). Recent reports differ regarding the regions on RxLR effector proteins involved in PIP recognition. To clarify these differences, I have structurally and functionally characterized the P. sojae effector, avirulence homolog-5 (Avh5). Using NMR spectroscopy, I demonstrate that Avh5 is helical in nature with a long N-terminal disordered region. Heteronuclear single quantum coherence titrations of Avh5 with the PtdIns(3)P head group, inositol 1,3-bisphosphate (Ins(1,3)P2), allowed us to identify a C-terminal lysine-rich helical region (helix 2) as the principal lipid-binding site in the protein, with the N-terminal RxLR (RFLR) motif playing a more minor role. Furthermore, mutations in the RFLR motif slightly affected PtdIns(3)P binding, while mutations in the basic helix almost abolished it. Avh5 exhibited moderate affinity for PtdIns(3)P, which increased the thermal stability of the protein. Mutations in the RFLR motif or in the basic region of Avh5 both significantly reduced protein entry into plant and human cells. Both regions independently mediated cell entry via a PtdIns(3)P-dependent mechanism. My findings support a model in which Avh5 transiently interacts with PtdIns(3)P by electrostatic interactions mainly through its positively charged helix 2 region, providing stability to the protein during RFLR-mediated host entry. / Ph. D.

In Escherichia coli, the utilization of glycerol and sn-glycerol 3-phosphate is mediated by gene products of the glp regulon. The regulon encompasses five operons, including the glpFKX operon. Although glpF and glpK encode glycerol diffusion facilitator and glycerol kinase,respectively, the function of glpX was unknown. In the present work, we show that glpX encodes a fructose 1,6-bisphosphatase (FBPase), which catalyzes the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate and phosphate. The purified FBPase was dimeric, dependent on Mn2+ for activity and exhibited an apparent Km of 35 μM for fructose 1,6-bisphosphate. The enzyme was inhibited by ADP, ATP and phosphate and activated by PEP. The attributes of the glpX-encoded FBPase were different from those of the previously characterized E. coli FBPase encoded by fbp. Mutants deleted in fbp (Δfbp) display a growthnegative phenotype on gluconeogenic carbon sources such as glycerol, indicating the inability of chromosomal glpX+ to complement Δfbp. However, a Δfbp mutation was complemented by overexpression of glpX+. In contrast, a glpX mutant exhibited a growth-positive phenotype on glycerol, glucose or fructose media. Surprisingly, a double mutant strain glpX pfkA (6-phosphofructokinase I) was more inhibited in growth on glucose and glycerol media than the pfkA parent. Carbohydrate metabolism in the pfkA background may be affected by the glpXmediated change in fructose 6-phosphate/fructose 1,6-bisphosphate levels. FBPase activities of soluble proteins separated by non-denaturing PAGE were visualized, showing a novel (third) FBPase, perhaps encoded by the glpX homolog, yggF. / Master of Science

Systemic acquired resistance (SAR) is a form of inducible defense response triggered upon localized infection that confers broad-spectrum disease resistance against secondary infections. Several factors are known to regulate SAR and these include phenolic phytohormone salicylic acid (SA), phosphorylated sugar glycerol-3-phosphate (G3P), and dicarboxylic acid azelaic acid (AzA). This study evaluated a role for free radicals nitric oxide (NO) and reactive oxygen species (ROS) in SAR. Normal accumulation of both NO and ROS was required for normal SAR and mutations preventing NO/ROS accumulation and/or biosynthesis compromised SAR. A role for NO and ROS was further established using pharmacological approaches. Notably, both NO and ROS conferred SAR in a concentration dependent manner. This was further established using genetic mutants that accumulated high levels of NO. NO/ROS acted upstream of G3P and in parallel to SA. Collectively, these results suggest that NO and ROS are essential components of the SAR pathway.

<p>DNA bases can be modified by endogenous agents (e.g. oxidized by products of respiration and photosynthesis or methylated by gene silencing processes) as well as by environmental agents (e.g. oxidized by UV light). In the process of removing modified bases, a 3’-phosphate group is sometimes left in the resulting gap, and has to be removed since it blocks the incorporation of a new nucleotide by DNA polymerase. The aim of this thesis was the characterization of AtZDP, a plant enzyme with a DNA 3’-phosphatase activity.</p><p>By homologous modeling, the existence of four domains was predicted in AtZDP, three independent zinc-finger and one DNA 3’-phosphatase domains. AtZDP was found to be localized in the nucleus by bimolecular fluorescence complementation. Western blotting analysis showed that the enzyme was ubiquitously expressed in plant tissues.</p><p>AtZDP was found in a 600,000 molecular-weight protein complex by gel chromatography and glycerol gradient sedimentation centrifugation. The fractions containing AtZDP in the complex displayed 3’-DNA phosphatase activity as shown by desphosphorylation of a DNA oligonucleotide with a 3’-phosphate terminus. Also fractions of the gel chromatography corresponding to lower molecular weight showed 3’-DNA phosphatase activity, but antibodies against AtZDP did not recognize this fraction inferring that in plants, at least another protein with similar activity exists.</p><p>In mammals, polynucleotide kinase, an enzyme with the same activity phosphatase activity as AtZDP, is involved in single-strand and double-strand repair pathways. To elucidate if AtZDP could be part of similar pathways, different double strand and single-strand oligonucleotides with 3’-phosphate termini were separately incubated with AtZDP. All substrates were dephosphorylated by AtZDP, assuming that this enzyme could potentially be involved in double-strand DNA repair. </p><p>A double-strand oligonucleotide containing a one-bp gap with a 3’-phosphate terminus was repaired by a leaf protein extract. The activities of a 3’-DNA phosphatase, a flap 5’ to 3’ endonuclease-like, a DNA polymerase and a DNA ligase were observed. The presence of these enzymes revealed that these damages are in plants predominantly repaired by long-patch base excision repair.</p>

DNA bases can be modified by endogenous agents (e.g. oxidized by products of respiration and photosynthesis or methylated by gene silencing processes) as well as by environmental agents (e.g. oxidized by UV light). In the process of removing modified bases, a 3’-phosphate group is sometimes left in the resulting gap, and has to be removed since it blocks the incorporation of a new nucleotide by DNA polymerase. The aim of this thesis was the characterization of AtZDP, a plant enzyme with a DNA 3’-phosphatase activity. By homologous modeling, the existence of four domains was predicted in AtZDP, three independent zinc-finger and one DNA 3’-phosphatase domains. AtZDP was found to be localized in the nucleus by bimolecular fluorescence complementation. Western blotting analysis showed that the enzyme was ubiquitously expressed in plant tissues. AtZDP was found in a 600,000 molecular-weight protein complex by gel chromatography and glycerol gradient sedimentation centrifugation. The fractions containing AtZDP in the complex displayed 3’-DNA phosphatase activity as shown by desphosphorylation of a DNA oligonucleotide with a 3’-phosphate terminus. Also fractions of the gel chromatography corresponding to lower molecular weight showed 3’-DNA phosphatase activity, but antibodies against AtZDP did not recognize this fraction inferring that in plants, at least another protein with similar activity exists. In mammals, polynucleotide kinase, an enzyme with the same activity phosphatase activity as AtZDP, is involved in single-strand and double-strand repair pathways. To elucidate if AtZDP could be part of similar pathways, different double strand and single-strand oligonucleotides with 3’-phosphate termini were separately incubated with AtZDP. All substrates were dephosphorylated by AtZDP, assuming that this enzyme could potentially be involved in double-strand DNA repair. A double-strand oligonucleotide containing a one-bp gap with a 3’-phosphate terminus was repaired by a leaf protein extract. The activities of a 3’-DNA phosphatase, a flap 5’ to 3’ endonuclease-like, a DNA polymerase and a DNA ligase were observed. The presence of these enzymes revealed that these damages are in plants predominantly repaired by long-patch base excision repair.

Thèse doctorat : Biologie Moléculaire : Nancy 1 : 2004. / Titre provenant de l'écran-titre.

Made available in DSpace on 2014-06-11T19:23:34Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-06-18Bitstream added on 2014-06-13T18:50:48Z : No. of bitstreams: 1 silva_vc_me_arafcf.pdf: 335369 bytes, checksum: 08eedc270c2e51ba9d6a9688bf400044 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O gene GPD2 de Saccharomyces cerevisiae, que codifica a enzima glicerol-3- fosfato desidrogenase (G3PDH; EC 1.1.1.8; NAD+: oxidoredutase) foi clonado na levedura Pichia pastoris para expressar extracelularmente a enzima em meio de cultura. Essa enzima apresenta aplicação prática em diversos sistemas acoplados para determinação quantitativa de triacilglicerol, glicerol, ácido fosfatídico e outros fosfolipidios também podendo ser usada para medir atividades enzimáticas em diversos tipos de amostras. Para que a atividade extracelular fosse suficiente em ensaios industriais e biológicos, um estudo de indução da expressão da enzima foi realizado no presente trabalho, que consistiu em escolher o clone que melhor secreta a enzima e estudar o meio de crescimento (BMGY), a densidade inicial celular (0,05 mg/mL), o meio de indução enzimática (BMMY), a natureza do tampão (tampão fosfato), o pH (6,0), o tempo de produção da proteína (4 dias), a concentração da enzima através de membrana filtrante (120 vezes), a melhor fonte de peptona (Acumédia), o estudo de pré-indução celular por estresse osmótico (atividade de 0,477 ± 0,0 U/mL em 24 horas com NaCl 0,35M). O processo de produção da G3PDH mostrou que a máxima produtividade enzimática (795 U/mL e atividade específica de 44,49 U/mg) e biomassa final de 17,75 mg/mL foi obtida com as seguintes condições experimentais: 48 horas de indução com meio BMMY, utilizando 1% de metanol, 1% de glicerol, densidade inicial celular de 0,05 mg/mL, pH 5,0 e sobrenadante concentrado 120 vezes em membrana filtrante. / The GPD2 gene from Saccharomyces cerevisiae, which encodes the enzyme glycerol-3-phosphate dehydrogenase (G3PDH, EC 1.1.1.8, NAD +: oxidoredutase) was cloned in the yeast Pichia pastoris to express the enzyme extracellularly in the culture medium. The enzyme G3PDH has practical application in various systems coupled to quantitative determination of triacylglycerol, glycerol, phosphatidic acid and other phospholipids. It can also be used to measure the enzymatic activities in diverse types of samples. For the application of the enzyme extracellular in industrial and biological tests, a study of induction of expression of the enzyme was accomplished in the present work, that consisted of to choose of clone that more expressing the enzyme, the growth medium (BMGY), the cellular initial density (0.05 mg/mL), the medium of enzymatic induction (BMMY), the buffer nature (phosphate potassium), pH (6.0), the time of production of the protein (4 days), the concentration of the protein (120-fold), the peptone source (Acumédia), the study of pre-induction cellular for osmotic stress (activity of 0.477 ± 0.0 U/mL in 24 hours with NaCl 0.35M). The study of the variable determinative in the process of production of the G3PDH it showed that the maximum enzymatic productivity (0.795 U/mL and 44.49 U/mg of specific activity) and final biomass of 17.75 mg/mL was obtained with the following experimental conditions: 48 hours of induction with medium BMMY, using 1% methanol, 1% glycerol, cellular initial density of 0.05mg/mL, pH 5.0 and the supernatant concentrated 120-fold in filter menbrane.

The thesis summarizes data gathered on various components of respiratory chain of Trypanosoma brucei. Namely, NADH:ubiquinone oxidoreductase (complex I), alternative NADH:ubiquinone oxidoreductase (NDH2) and mitochondrial glycerol-3-phosphate dehydrogenase are discussed themselves and in broader context of energy metabolism. Also, a work done using RNA interference library is described.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第18346号 / 農博第2071号 / 新制||農||1024(附属図書館) / 学位論文||H26||N4853(農学部図書室) / 31204 / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 栗原 達夫, 教授 植田 充美, 教授 小川 順 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM