One purpose of this study was to determine whether the ras protein from Dictyostelium discoideum (p23) binds guanine nucleotides like the ras proteins from mammals (p21) and yeast. The other purpose of this investigation was to purify or enrich for p23ras from D. discoideum by immunoaffinity chromatography. A number of different approaches were used to determine guanine nucleotide binding by p23RAS . A simple filter binding assay, binding to Western blots, and photoaffinity labeling all failed to demonstrate specific binding with lysates of D. discoideum cells. In contrast p21RAS from transformed NIH-3T3 cell lysate was successfully photoaffinity labeled in the presence of ³²P-α-guanosine 5¹-triphosphate (GTP) suggesting that the technique had been performed correctly. It was concluded that either p23RAS has a very low affinity for guanine nucleotides such that GTP binding was not detectable in these experiments or that the ras protein from D. discoideum simply does not bind guanine nucleotides. The purification of p23RAS from D. discoideum cells was attempted in order to provide a purified protein preparation for guanine nucleotide binding and for reconstitution studies. An anti-ras monoclonal antibody (Y13-259) was used as the ligand for the immunoaffinity chromatography. This approach was not successful in that the ras protein could not be enriched relative to other proteins because the immunoaffinity columns did not bind p23RAS. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

The role of cyclic AMP and a differentiation-indueing factor (DIF) in the differentiation of stalk cells was investigated in the cellular slime mold Dictyostelium discoideum. In this organism, starvation triggers the aggregation of amoebae into multicellular masses within which a simple, well-regulated pattern of partially differentiated cells is formed and which ultimately form fruiting bodies comprised of spore and stalk cells. In a monolayer system at low cell densities, stalk cell formation is dependent on the presence of both cyclic AMP and DIF. Both factors act within a short time of each other, induction by cyclic AMP preceding induction by DIF, beginning between 8 to 10 hours of incubation in monolayers, and progressively committing an increasing proportion of the cells in monolayer to form stalk cells. The relative effectiveness of analogues of cyclic AMP to induce stalk cell formation in monolayers indicates that the well-characterized cell surface cyclic AMP receptor most probably mediates the action of cyclic AMP. Although this receptor appears early during aggregation, it does not become activated until later during development in vivo, probably because the cyclic AMP concentrations within developing cell masses must build up to levels higher than those in aggregation streams. The finding that caffeine inhibits stalk cell formation in low density monolayers and that the permeable analogue 8-Bromo-cyclic AMP can partially reverse this inhibition suggests that activation of this receptor leads to an increase in internal cyclic AMP levels as one of the steps in stalk cell differentiation. The finding that the expression in low density monolayers of AP IV, a cell-type non-specific isozyme of acid phosphatase, was cyclic AMP-dependent is consistent with the view that cyclic AMP induces non-specific postaggregative gene expression during development in vivo. The findings that the expression of pre-stalk arid stalk cell specific antigens and of the pre-stalk cell specific isozyme AP II was DIF-dependent provide good evidence for the idea that both pre-stalk and stalk cell formation are induced by DIF. The fact that isolated pre-stalk cells require DIF for stalk cell formation in low density monolayers further supports this idea. Whereas cells independent of DIF for stalk cell formation in monolayers appear immediately after cyclic AMP-independent cells during differentiation in low density monolayers, DIF-independent cells appear considerably later during development in vivo. This evidence and the fact that developing cell masses contain elevated levels of DIF lead to the postulate that the factor(s) which triggers the formation of fruiting bodies also controls the pre-stalk to stalk cell conversion. / Science, Faculty of / Botany, Department of / Zoology, Department of / Graduate

Dictyostelium discoideum (Dd) is a model organism, studied for reasons from cell movement to chemotaxis to human disease control. Creating a computer model of the life cycle of Dd has garnered great interest, one part of which is the Aggregation Stage, where thousands of amoeba gather together to form a slug. Chemotaxis is the mechanism through which this is accomplished. This thesis develops two- and three-dimensional alternating direction implicit code which solves the diffusion equation on an adaptive grid. The calculated values for both two and three dimensions are checked against the actual solution and error results are provided. Comparisons are made between the coarse grid with refinement case and a fine grid without refinement case. Also, a non-negativity condition for two dimensions is derived to give a bound on the three major parameters: the diffusion coefficient and the spatial and time discretizations.

The cellular slime mold, <i><b>Dictyostelium discoideum</i></b>, has two developmentally regulated forms of the enzyme glycogen phosphorylase, which are encoded by two distinct, but related genes (Rutherford, et. aI., 1991). A complementary DNA (cDNA) encoding glycogen phosphorylase-}, gp-l, was isolated from a λgtll expression library made from amoebae stage mRNA. The 5' upstream region of the gp-l gene was cloned by inverted polymerase chain reaction (IPCR) and partial genomic DNA library screening. The gp-l gene was found as one copy or low copy number gene in the <i><b>Dictyostelium</i></b> genome, and an adjacent 22 kilobase pair region was physically mapped. The deduced amino acid sequencing analysis revealed that there were 862 amino acid residues encoded by the gp-1 mRNA of 2729 nucleotides. It was also found that most regulatory and catalytic domains were similar to those in other glycogen phosphorylases. One intron of 139 bp was verified beginning after the 40th amino acid codon. The transcriptional start site was determined at 134 nucleotides upstream of the ATG initiation codon. Gel retardation assays demonstrated that there were at least two nuclear DNA binding proteins from vegetative amoebae (V 1 and V2 factors) and two from developing cells (D 1 and D2 factors). Experiments with a luciferase reporter gene suggested that a basal expression of the gp-l gene can be conferred by the 5' region containing 363 bp upstream of the ATG codon and the entire regulatory region is located at 157 to 700 bp upstream of the ATG site. It was also demonstrated that the 363 bp deletion fragment did not support cyclic AMP (cAMP) responsiveness of the gp-l gene. DNase I footprinting mapped two regions that were protected by nuclear DNA binding proteins and one of them was a palindromic sequence: CAAGTCGCTIG. / Ph. D.

Ultra-microfluorometric techniques were adapted to follow several compounds related to energy metabolism through the developmental cycle of Dictyostelium discoideum. Each compound (ATP, trehalose, glucose, and ammonium ion) was found to be present in stalk and/or spore cells. The accumulation of NH₄⁺ was interpreted as an indication of protein degradation, a source of energy in this organism. During the early stages of differentiation NH₄⁺ was localized only in stalk cells. However, it accumulated in spore cells during culmination such that levels were comparable in the two cell types by the end of development. Trehalose, an energy source for germinating spores, was found in both cell types but was preferentially degraded in stalk cells late in development. Glucose, the degradation product of trehalose, was localized in stalk cells and varied inversely with trehalose in prestalk cells. ATP was not localized in a specific cell type during development. However, ATP declined in stalk cells at an earlier stage of development. These findings emphasize the need for knowledge of cell-specific events involved in the differentiation of this and other organisms. / Master of Science

Multi-Agent Systems (MASs) and Partial and Ordinary Differential Equations (PDEs and ODEs respectively) have often been employed by researchers to effectively model and simulate Complex Adaptive Systems (CASs). PDEs and ODEs are reduction based approaches which view the system globally and ignore any local interactions and processes. MASs are considered by many to be a better tool to model CASs, but have issues as well. Case in point, there is concern that present day MASs fail to capture the true essence of inter-cellular communication in a CAS. In this work we present a realistic and utilizable communication framework for inter-agent communication for a CAS simulation. We model the dynamic properties of the communication signals and show that our model is a realistic model for inter-cellular communication. We validate our system by modeling and simulating pattern formation in Dictyostelium discoideum, a unicellular organism. / Master of Science

Cyclic AMP functions as the chemotactic signal during aggregation of single-celled amoebae of the cellular slime mold Dictyostelium discoideum. Evidence suggests that cyclic AMP also acts as a regulatory molecule during Dictyostelium multicellular differentiation. Biochemical characterization of adenylate cyclase, the cyclic AMP synthetic enzyme, was accomplished using a sensitive radioimmunoassay. The enzyme was found to be pellet-bound. The non-ionic detergents, Triton X-100 and Lubrol PX, were not effective for solubilizing this activity. Magnesium or manganese could serve as the required divalent cation, with the Mn-supported activity over 4-fold greater than the Mg-supported activity. Typical mammalian adenylate cyclase modulators such as guanyl nucleotides, fluoride, and cholera toxin did not activate the Dictyostelium enzyme. Calcium, in conjunction with its protein receptor calmodulin, did not appear to regulate the enzyme. An endogenous extracellular, heat-stable substance was found to inhibit Dictyostelium adenylate cyclase. By use of ultramicrotechniques adenylate cyclase activity was localized in the pre-spore cells of the culminating individual with no activity detected in the pre-stalk region. Lack of detectable activity in the pre-stalk cells may be due to a masking by the endogenous inhibitor. An increasing gradient of activity was found in the pre-spore mass with activity increasing from the uppermost area to the base. No striking localization was seen prior to the pre-culmination stage of development. Two peaks in cyclic AMP levels, as measured in individuals were found during development. One coincided with aggregation, the other occurred at the culmination stage. A gradient of cyclic AMP within the culminating individual paralleled the gradient of adenylate cyclase activity. The tip of the individual had greater levels of cyclic AMP than the middle pre-spore region, and the upper stalks had higher levels than the lower stalks. These data indicate an enzymatic potential for establishing a gradient of cyclic AMP. At the culmination stage of development this molecule could act to direct the chemotactic movements of the pre-stalk cells as well as provide positional information for the terminal differentiation of the pre-spore cells into mature spores. / Ph. D.

The slime mold Dictyostelium discoideum has two developmentally regulated forms of the enzyme glycogen phosphorylase. The inactive ’b’ form requires 5'AMP for activity and is present in early development, whereas the active ’a’ form is 5'AMP independent and is present in late development. Polyclonal antibodies raised to purified forms of the enzyme show low cross-reactivity. The anti-’a’ is specific for a 104 kd protein associated with phosphorylase ‘a’ activity; the anti-’b’ is specific for a 92 kd protein associated with the ’b’ activity. The two antibodies inhibit the activities of their corresponding antigens, furthermore, each antibody recognizes the proteolytic products of its corresponding antigen. In the presence of exogenously added Mn²⁺ and ATP, the ‘b’ form shows apparent conversion to a 5'AMP independent form as detected spectrophotometrically. This apparent conversion is accompanied by in vitro phosphorylation of the ’b’ enzyme by a Mn²⁺ dependent protein kinase. The ’b’ kinase also phosphorylates casein in the presence of Mg²⁺ or Mn²⁺. In vivo phosphorylation of the ’b’ form was observed in early development. Phosphorylation of the ’b’ form did not result in the appearance of the 104 kd protein. At this point, it is unclear whether Dictyostelium phosphorylase ’a’ represents a phosphorylated and activated form of the ’b’ form, or whether it represents a separate gene product. / Ph. D.

As proteínas fosfatases são enzimas responsáveis pela desfosforilação de resíduos de fosfoaminoácidos, principalmente fosfotirosina e fosfoserina/treonina, o que divide esta classe de proteínas nas famílias PTP (proteína tirosina fosfatase) e PP (proteína serina/treonina fosfatase). Diversos membros da família das PPs, em particular da subfamília PPP (Phosphoprotein Phosphatase), existem como holoenzimas compostas de uma subunidade catalítica associada a uma ou mais subunidades reguladoras, que lhes conferem diversidade funcional. Neste trabalho tivemos como objetivo identificar, utilizando ensaios no sistema de duplo híbrido em leveduras, proteínas que interagem com as subunidades catalíticas das serina/treonina fosfatases do tipo 1 (DdPP1c) e do tipo 4 (DdPP4c) da ameba social D. discoideum. Varreduras de bibliotecas de cDNA das fases de crescimento e desenvolvimento da linhagem AX4 de D. discoideum com as iscas DdPP1c e uma variante mutante da DdPP1c (DdPP1cF269C) possibilitaram a identificação de pelo menos 30 genes com evidência de interação com a PP1c. A varredura das bibliotecas com a isca DdPP4 propiciou a identificação de 10 potenciais genes candidatos com evidência de interação com a PP4c. Várias dos candidatos identificados nas varreduras correspondem a genes que codificam para proteínas hipotéticas que não apresentam similaridade significativa com proteínas de função conhecida. Entre essas, identificamos e caracterizamos DdI-3, um ortólogo do inibidor-3 da PP1c de mamíferos. A interação de DdI-3 com DdPP1c foi confirmada através de ensaios independentes no sistema do duplo híbrido em leveduras. Demonstramos que DdI-3 recombinante expresso em bactérias possui atividade inibidora da DdPP1c in vitro, sendo que esta enzima tem 50% de sua atividade de fosforilase fosfatase inibida por cerca de 0,55 nM de rDdI-3. Estes dados indicam que DdI-3 é 50 vezes mais potente do que DdI-2, um ortólogo do inibidor-2 previamente caracterizado em D. discoideum. Neste trabalho, também iniciamos a construção do catálogo (The Dictyostelium Phosphatome) que irá conter todas as subunidades catalíticas e reguladoras das proteínas fosfatases codificadas no genoma de D. discoideum. Até o momento, 101 genes foram catalogados e classificados nas diferentes famílias das proteínas fosfatases, sendo 16 na família das PTPs, 26 na família das DSPs (proteína fosfatase de dupla especificidade), 15 na família das PPMs (Phosphoprotein Phosphatase Magnesium-dependent) e 31 na família das PPPs, incluindo genes codificadores de subunidades catalíticas e reguladoras. / Protein phosphatases are responsible for dephosphorylating phosphoaminoacids residues, notably phosphotyrosine and phosphoserine/threonine, thus dividing these enzymes into PTP (protein tyrosine phosphatase) and PP (protein serine/threonine phosphatase) families. Several members of the PP family, in particular those belonging to PPP (Phosphoprotein Phosphatase) are composed of one catalytic subunit and one or more regulatory subunits that provide functional diversity to the holoenzyme. In this work our goal was to identify protein interactors to type 1 (DdPP1c) and type 4 (DdPP4c) phosphatase that might behave as potential regulatory subunits of these enzymes in the social amoeba Dictyostelium discoideum. For this intent, DdPP1c, a mutant isoform of DdPP1 (DdPP1cF269C) and DdPP4c were used as baits in yeast two-hybrid based screening of D. discoideum (AX-4 strain) cDNA libraries from growth as well as developmental stages. At least 30 genes were identified as potential DdPP1c interactors while 10 genes were selected as candidates to interact to DdPP4c. Most of them are currently annotated in D. discoideum genome as hypothetical proteins of unknown function. Among the potential PP1c interactors we selected DdI-3, an ortholog of mammalian inhibitor-3. Interaction of DdI-3 and DdPP1c was confirmed by independent yeast two-hybrid assays. We demonstrated that bacterial expressed recombinant DdI-3 is effective as an inhibitor of DdPP1c in vitro, since 50% of DdPP1c phosphorylase phosphatase activity is inhibited by circa 0,55 nM of purified rDdI-3. Our results also showed that DdI-3 is 50 times more effective than DdI-2, a previously characterized PP1c inhibitor in D. discoideum. In this work we began to organize The Dictyostelium Phosphatome, a catalog of all protein phosphatases, including their catalytic and regulatory subunits, encoded in D. discoideum genome. Until now, we have classified 101 genes into the protein phosphatase families, of which 16 were classified as classic PTP, 26 as DSP (dual-specificity phosphatases), 15 as PPM (Phosphoprotein Phosphatase Magnesium-dependent) and 31 as PPP, including genes for catalytic as well as regulatory subunits.

A serina/treonina fosfatase do tipo 1 (PP1) é uma enzima ubíqua nas células e nos tecidos das várias espécies em que foi pesquisada e regula vários processos como metabolismo intermediário, processamento de mRNA, transcrição e apoptose. Geralmente a holoenzima PP1 é encontrada como um dímero constituído por uma subunidade catalítica conservada (PP1c) e uma ou mais subunidades reguladoras variáveis. Em mamíferos, já foram identificados mais de 50 polipeptídeos que se associam direta ou indiretamente a PP1c, gerando holoenzimas com localizações celulares e especificidades distintas. Entre estas proteínas estão inibidores citosólicos de PP1c, tais como o inibidor-1 (I-1), o inibidor-2 (I-2) e o inibidor nuclear da PP1 (NIPP-1). Ortólogos do I-2 foram descritos em microorganismos como Saccharomyces cerevisiae e Neurospora crassa. Neste trabalho nós demonstramos que o genoma da ameba social Dictyostelium discoideum possui uma única cópia do gene que codifica um ortólogo do I-2 (DdI-2). Análise através de Northern blot mostrou que o mRNA de DdI-2 é expresso durante o crescimento e ao longo de todo o ciclo de desenvolvimento, com níveis variáveis. Também demonstramos que o gene DdI-2 codifica uma verdadeira proteína inibidora da PP1c uma vez que seu produto recombinante em bactéria é capaz de inibir, com eficácia equivalente, as atividades de fosforilase fosfatase das PP1c recombinantes selvagem (DdPP1c) e mutante (DdPP1cF269C) de D. discoideum e NcPP1c de N. crassa in vitro. A proteína DdPP1cF269C apresenta características distintas da DdPP1c incluindo maior estabilidade, maior atividade de fosforilase fosfatase e maior sensibilidade frente ao inibidor caliculina A. Estas diferenças devem-se a substituição da cisteína conservada da posição 269 por uma fenilalanina, que é verificada na enzima selvagem. DdPP1c e DdPP1cF269C foram também ensaiadas na presença de INc-1L e INc-1 que são ortólogos de I-2 em N. crassa. Ambas as proteínas recombinantes purificadas exibiram efeito inibidor sobre a atividade de fosforilase fosfatase das DdPP1c recombinantes selvagem e mutante, sendo que INc-1 foi um inibidor duas vezes mais eficiente que INc-1L. Este efeito pode ser devido a um segmento de 38 aminoácidos codificado por um íntron em fase que é retido na isoforma INc-1L. Nossos dados indicam ainda que a mutação F269C não afetou a sensibilidade da DdPP1c recombinante a nenhum dos ortólogos de I-2 testados in vitro. Ensaios de duplo-híbrido utilizando a PP1c selvagem e mutante de D. discoideum (DdPP1c e DdPP1cF269C) e de N. crassa (NcPP1c) como iscas e DdI-2 como presa mostraram que estas proteínas interagiram in vivo. Quando a presa era o INc-1L ou INc-1 a interação ocorreu apenas com a NcPP1c, sendo mais forte no caso de INc-1. As regiões de DdI-2 envolvidas na interação física com a DdPP1c foram mapeadas através da expressão de proteínas truncadas no ensaio de duplo híbrido. Os experimentos apontaram que o carbóxi-terminal de ~100 aminoácidos não é essencial para a interação, mas que o somatório das diversas regiões responde pela integridade da interação. / The serine/threonine phosphatase of type-1 (PP1) is a ubiquous enzyme in the cells and tissues from several species studied and regulates numerous processes such as intermediate metabolism, mRNA splicing, transcription, and apoptosis. PP1 holoenzymes consist of a well-conserved catalytic subunit (PP1c) and one or more variable regulatory subunits. In mammals, more than fifty polypeptides that bind PP1c have been identified, originating holoenzymes with distinct cell locations and specificities. These proteins include cytosolic PP1c inhibitors such as inhibitor-1 (I-1), inhibitor-2 (I-2) and nuclear inhibitor of PP1 (NIPP-1). I-2 orthologs have also been described in Saccharomyces cerevisiae and Neurospora crassa. In the present work, we demonstrate that the genome of the social amoeba Dictyostelium discoideum has a single gene encoding for an I-2 ortholog (DdI-2). Northern blot analyses have shown that DdI-2 mRNA is expressed throughout Dictyostelium developmental cycle at variable levels. We also demonstrated that DdI-2 is a true PP1c inhibitor as its recombinant product is capable of inhibiting the phosphorylase phosphatase activity of wild-type PP1c (DdPP1c) and mutant (DdPP1cF269C) of D. discoideum and NcPP1c of N. crassa in vitro. DdPP1cF269C protein presents distint traits including higher stability, phosphorylase phosphatase activity and sensibility to calyculin A than the wild-type. These differences are originated from the replacement of a well conserved cisteine residue by a phenylalanine found in the wild-type. The wild-type and mutant DdPP1c have also been assayed in the presence of INc-1L and INc-1 which are orthologues to I-2 in N. crassa. Both purified recombinant proteins have shown inhibitory effects over phosphorylase phosphatase activities, with INc-1 being twice more potent than INc-1L. This might be due to the presence of an intron retention event in the latter that results in a insertion of 38 aminoacids. Our data also indicate that F269C mutation did not affect DdPP1c sensitivity to inhibition by all the three recombinant I-2 orthologues in vitro. Yeast two-hybrid assays using wild type (DdPP1c) and mutant (DdPP1cF269C) D. discoideum and N. crassa (NcPP1c) PP1c as preys and the putative inhibitor DdI-2 as a bait showed inequivocally that these proteins interacted in vivo. When the prey was INc-1 or INc-1L the interaction occured only with NcPP1c and was stronger with INc-1. The domains of DdI-2 involved in the interaction with DdPP1c were mapped by two-hybrid interaction assays with DdI-2 deleted mutants. These experiments have pointed out that the DdI-2 carboxi-terminus of ~100 aminoacids is not essential for the interaction but that the sum of all regions is responsible for the integrity of the interaction.