DictyMOLD-a Dictyostelium discoideum genome browser database

SUMMARY: With the Dictyostelium Genome Project nearing completion, we initiated the construction of a data repository for all Dictyostelium discoideum genomic data. Up to now this database, called DictyMOLD (Dicty Map Of Linked Data), incorporates the recently completed D.discoideum chromosomes 1 and 2 sequences together with related annotations. To visualise maps, sequences and annotations and to provide access for the scientific community a perl-based browser was developed. AVAILABILITY: The DictyMOLD database is freely accessible via http://genome.imb-jena.de/dictyostelium/ CONTACT: gernot@imb-jena.de.     

Genomic organization of the transposable element Tdd-3 from Dictyostelium discoideum.

The transposable element Tdd-3 from D. discoideum has been described originally in 1984 (Poole and Firtel, 1984). Additional copies of this element were discovered in the course of a recent study on tRNA gene organization in D. discoideum. Five out of 24 independently isolated tRNA genes proved to be associated with Tdd-3 elements. The surprising observation that all the elements always occurred within the 3'-flanking sequences of the Dictyostelium tRNA genes suggested the possibility of a general position specific integration of Tdd-3 elements upon transposition. Therefore we isolated additional Tdd-3 elements from various genomic D. discoideum libraries in order to test this hypothesis. Several new Tdd-3 elements were found associated with various tRNA genes. Additionally we identified Tdd-3 elements organized in tandem array or in association with RED (Repetitive Element of Dictyostelium), another repetitive element recently identified by our laboratory. In all cases a B-box equivalent of the eukaryotic gene-internal RNA polymerase III promoter was identified upstream of all Tdd-3 elements.     

Chemiluminescence in Dictyostelium discoideum

Abstract Oxygen radicals generated during oxidative metabolism participate in chemical reactions resulting in light emission. Chemiluminescence is used therefore to measure their production. We have shown that starvation and heat shock induce chemiluminescence in Dictyostelium discoideum . The peak light emission was found to occur about 4 h after the onset of starvation. The optimum temperature for chemiluminescence by starving amoebae was about 33°C. The heat shock inducibility of chemiluminescence was maximal at the beginning of development. Our results are consistent with suggestions that the product(s) of perturbed mitochondrial metabolism might be intracellular signal(s) controlling gene expression in stressed cells. They also suggest a role for intracellular stress signal(s) in the initiation of development in Dictyostelium by starvation.     

Aggregation in Dictyostelium discoideum

Cultured peritoneal macrophages have previously been shown to release a potent mitogen for mesenchymal cells. Peritoneal macrophages are derived from peripheral blood monocytes, one of the principal inflammatory cells associated with numerous tissue responses to injury. Cultured human monocytes can be activated by endotoxin or concanavalin A to secrete a potent growth factor(s) that is active on human smooth muscle cells, human fibroblasts and 3T3 cells. The optimal conditions for activation of monocyte release of this monocyte-derived growth factor(s) (MDGF) were to expose 5-day-old monocyte cultures (initially plated at 6.8 × 10⁵ cells/ml medium) to 10 μg/ml endotoxin or 6 μg/ml concanavalin A for approximately 20 hr. Monocytes can secrete MDGF into serum-free medium supplemented with 0.15% bovine serum albumin. MDGF stimulates both DNA synthesis and increase in cell number and is trypsin-sensitive, heat labile and nondialyzable. The relationship of MDGF to other monocyte products and its potential importance in wound repair and atherogenesis are discussed.     

Cell-cell adhesion in Dictyostelium discoideum

Three separate mechanisms of cell-cell adhesion have been shown to appear at different stages of development in Dictyostelium discoideum. During the first few hours of development, the cells synthesize and accumulate a glycoprotein of 24,000 daltons (gp24) that is positioned in the membrane. The time of appearance of gp24 correlates exactly with the time of appearance of cell-cell adhesion in two strains in which temporal control varies by several hours. Antibodies specific to gp24 are able to block cell-cell adhesion during the first few hours of development but not during later development. By 8 hr of development, another glycoprotein, gp80, that is not recognized by antibodies to gp24 accumulates on the surface of cells. This membrane protein mediates an independent adhesion mechanism during the aggregation stage that is resistant to 10 mM EDTA. Antibodies specific to gp80 can block EDTA-resistant adhesion during this stage. During subsequent development, gp80 is removed from the cell surface and replaced by another adhesion mechanism that is insensitive to antibodies to either gp24 or gp80. A lambda gt11 expression vector carrying a Dictyostelium cDNA insert was isolated that directs the synthesis of a fusion protein recognized by antibodies specific to gp24. This cDNA was used to probe a genomic library. A clone carrying a 1.4-kb insert of genomic DNA was recognized by the cDNA and shown to hybridize to a 0.7-kb mRNA that accumulates early in development. This unusually small RNA could code for the small protein, gp24. Southern analysis of restriction fragments generated by various enzymes on Dictyostelium DNA with both the cDNA and genomic clones indicated the presence of two tandem copies of the gene. This may account for the failure to recover mutations resulting in the lack of gp24. Mutations have been recovered that result in the lack of accumulation of gp80, and cells carrying these mutations have been shown to be missing the second adhesion mechanism. These mutant strains are able to complete development because the other adhesion mechanisms are not impaired. Sequential addition of adhesion mechanisms provides a means for the formation of multicellular organisms from previously solitary cells.     

Temperature-sensitive mutants of Dictyostelium discoideum

Three classes of temperature-sensitive mutants of the cellular slime mold Dictyostelium discoideum have been isolated. One class contains strains able to grow at 22 C but not at 27 C. Cells of these strains can develop into sorocarps at both temperatures. Another class contains strains which can grow at both temperatures but can only develop at the lower temperature. The third class contains strains unable to grow or develop at 27 C. Those strains whose development is temperature-sensitive appear to carry mutations which affect the cells only during the period of aggregation before the construction of a multicellular sorocarp. When pairs of growth-temperature-sensitive (GTS) strains develop in mixed aggregates, temperature-resistant (TR) cells are formed at a frequency of about 10(-4). These TR cells transmit the phenotype in a relatively stable hereditary fashion. However, temperature-sensitive segregants can be isolated from TR strains even after six clonal passages. Mixed incubation of pairs of morphologically aberrant GTS strains was found to give rise to TR progeny which develop normally. These progeny clones independently segregate morphologically aberrant strains and temperature-sensitive strains. The results indicate that several temperature-sensitive and morphological mutations are recessive and nonidentical.     

Developmental commitment in Dictyostelium discoideum

Upon starvation, Dictyostelium discoideum cells halt cell proliferation, aggregate into multicellular organisms, form migrating slugs, and undergo morphogenesis into fruiting bodies while differentiating into dormant spores and dead stalk cells. At almost any developmental stage cells can be forced to dedifferentiate when they are dispersed and diluted into nutrient broth. However, migrating slugs can traverse lawns of bacteria for days without dedifferentiating, ignoring abundant nutrients and continuing development. We now show that developing Dictyostelium cells revert to the growth phase only when bacteria are supplied during the first 4 to 6 h of development but that after this time, cells continue to develop regardless of the presence of food. We postulate that the cells' inability to revert to the growth phase after 6 h represents a commitment to development. We show that the onset of commitment correlates with the cells' loss of phagocytic function. By examining mutant strains, we also show that commitment requires extracellular cyclic AMP (cAMP) signaling. Moreover, cAMP pulses are sufficient to induce both commitment and the loss of phagocytosis in starving cells, whereas starvation alone is insufficient. Finally, we show that the inhibition of development by food prior to commitment is independent of contact between the cells and the bacteria and that small soluble molecules, probably amino acids, inhibit development during the first few hours and subsequently the cells become unable to react to the molecules and commit to development. We propose that commitment serves as a checkpoint that ensures the completion of cooperative aggregation of developing Dictyostelium cells once it has begun, dampening the response to nutritional cues that might inappropriately block development.     

Discoidin-binding polysaccharide from Dictyostelium discoideum

Extracts of Dictyostelium discoideum grown axenically in a chemically defined medium were evaluated for binding to discoidin I and discoidin II, endogenous lectins of this slime mold. Binding activity was measured by competitive inhibition of 125I-lactosyl-bovine serum albumin binding to the immobilized lectins. With the solubilization procedure used extracts of vegetative cells and of early aggregates had no significant inhibitory activity, but an abundant discoidin-binding substance was detected in late aggregates and fruiting bodies. This material was purified by ethanol and acid precipitation followed by precipitation with discoidin. It is a polysaccharide composed of 77% galactose, 15% N-acetylgalactosamine, 5% glucose, and 3% N-acetylglucosamine and may be a biologically functional ligand for the slime mold lectins, in particular discoidin II. Use of axenic cells was critical in these experiments, since extracts of Escherichia coli and Klebsiella aerogenes, commonly used as food for D. discoideum, were found to contain substances that react with discoidin. This would complicate isolation of endogenous discoidin ligands from cells raised on bacteria.     

Cell Differentiation in Dictyostelium discoideum

We have shown previously that amoebae of D. discoideum strain V12 M2 starved at low density in the presence of cyclic AMP fail to form either stalk cells or prespore cells; a low molecular weight factor released by cells at high density promotes stalk formation under these conditions but formation of prespore cells requires 'cell contact'. Here we summarise evidence that:
1. Elevated intracellular cyclic AMP levels are required for all developmental gene expression beyond the preaggregative phase, and ammonia antagonises this expression in some way. However, the action of ammonia is not pathway specific.
2.'Cell contact' is a specific requirement for entry into the prespore pathway of gene expression since isolated cells provided with cyclic AMP synthesise much reduced amounts of the presporespecific enzyme uridine diphosphate (UDP) galactose polysaccharide transferase but normal amounts of the pathway-indifferent enzyme glycogen phosphorylase.
3. The 'cell contact' mechanism is uniquely sensitive to low concentrations of pronase. This protease selectively inhibits transferase synthesis and blocks in vitro spore differentiation (in a spore-forming mutant). It does not prevent chemotactic aggregation, stream formation, or stalk cell formation in the presence of cyclic AMP.     

Spore germination in Dictyostelium discoideum

Mutant spores of Dictyostelium discoideum, strain SG-10, differ from wild type spores in their ability to spontaneously germinate, to be activated with 5% dimethyl Sulfoxide (DMSO), and to be deactivated with 0.2 M sucrose. Both heat-activated wild type and mutant spores began to swell after a lag of 60–75 min at ambient temperature. Suspension of heat activated spores in 5% DMSO resulted in blockage of spore swelling and a concomitant severe inhibition of respiration; removal of 5% DMSO allowed resumption of respiration and the spores began to swell after a lag of only 15 min. It was concluded that 5% DMSO allowed the early reactions (M) to proceed but blocked the later reactions (R) of post-activation lag.Treatment of one day old spores with 20% DMSO solution for 30–120 min quantitatively activated the population. The post-activation lag time was directly dependent on the time of 20% DMSO treatment. Spores activated with 20% DMSO treatment could be deactivated by incubation at 0°C; the spores most quickly deactivated at 0°C were those within 10 min of swelling. Mitochondrial transport inhibitors such as azide and cyanide caused deactivation in an analogous manner. It is hypothesized that spores proceed to the second portion of the lag phase called (R) before the environment determines if dormancy is reimposed or if germination will proceed. The sensitive strain (SG-10) showed a greater degree of damage than the wild type after supraoptimal treatment with 40% DMSO. The spores became more resistant with age to the damaging action of 40% DMSO. All the observed effects of DMSO treatment were compatible with our multistate model of activation which suggests that the early portion of the lag phase (M) may involve a relative uncoupling of oxidative phosphorylation while the later portion (R) may require tight coupling.     

Nonsense suppression in Dictyostelium discoideum

We describe the generation of Dictyostelium discoideum cell lines that carry different suppressor tRNA genes. These genes were constructed by primer-directed mutagenesis changing a tRNA(Trp)(CCA) gene from D. discoideum to a tRNA(Trp)(amber) gene and changing a tRNA(Glu)(UUC) gene from D. discoideum to a tRNA(Glu)(ochre) as well as a tRNA(Glu)(amber) gene. These genes were stably integrated into the D. discoideum genome together with a reporter gene. An actin 6::lacZ gene fusion carrying corresponding translational stop signals served as a reported. Active beta-galactosidase is expressed only in D. discoideum strains that contain, in addition to the reporter, a functional suppressor tRNA. Both amber suppressors are active in D. discoideum without interfering significantly with cell growth and development. We failed, however, to establish cell lines containing a functional tRNA(Glu)(ochre) suppressor. This may be due to the fact that nearly every message from D. discoideum known so far terminates with UAA. Therefore a tRNA capable of reading this termination codon may not be compatible with cell growth.     

Acid Phosphatase in Dictyostelium discoideum

An acid phosphatase has been studied at various stages of development of Dictyostelium discoideum. This enzyme has a pH optimum of 3.6 and catalyses the hydrolysis of both hexose phosphates and mononucleotides as well as that of p-nitrophenyl phosphate. The enzyme specific activity increases 2–4 fold in vitro during differentiation, but the activity in vivo may be controlled through endproduct inhibition by orthophosphate, which accumulates in the cells during sorocarp formation. The predicted activity in vivo is highest in the middle of development, especially at the pre-culmination stage.     

Ras-related genes in Dictyostelium discoideum

Dictyostelium discoideum, like other eukaryotes, has been shown to express several ras-related genes. Two gene products, Ddras and DdrasG, are highly conserved relative to the human ras proteins. Ddras is expressed at the pseudoplasmodial stage of development, whereas DdrasG is expressed in vegetative cells and during early development. In addition, Dictyostelium possesses three ras-related genes, SAS1, SAS2 and Ddrap1, whose gene products are only partially conserved relative to those of the ras genes. The expression of these three genes is also developmentally regulated.     

Prespore-inducing factors in Dictyostelium discoideum

Abstract. In an attempt to investigate the pathway of prespore differentiation in the cellular slime mold, Dictyostelium discoideum , we examined the requirements for prespore differentiation under conditions involving no cellular interactions. Aggregation-competent cells of the wild-type NC4 strain incubated in an isolated state were found to differentiate into prespore cells depending on the presence of cAMP, bovine serum albumin, and the prespore inducing factors (PIF) obtained from the conditioned media. Vegetative cells did not differentiate into prespore cells under these conditions. The prespore-inducing activity found in extracts of cells was developmentally regulated and induced by cAMP. PIF was of a low molecular mass (150–400 kilodaltons), was heat, alkali, and acid stable, and was extractable from an acidified water phase using ethylacetate. Purification of the PIF in ethylacetate extracts by gel-permeation chromatography followed by reverse-phase chromatography revealed two major peaks with prespore-inducing activity. On mixing these two fractions, the original activity was restored, indicating that PIF is composed of at least two components.     

Phagosomal Proteins of Dictyostelium discoideum

ABSTRACT. In recognizing food particles, Dictyostelium cell-surface molecules initiate cytoskeletal rearrangements that result in phagosome formation. After feeding D. discoideum cells latex beads, early phagosomes were isolated on sucrose step gradietns. Protein analyses of these vesicles showed that they contained glycoproteins and surface-labeled species corresponding to integral plasma membrane proteins. Cytoskeletal proteins also were associated with phagosomes, including myosin II, actin and a 30 kDa-actin bundling protein. As seen by the acridine orange fluorescence of vesicles containing bacteria, phagosomes were acidified rapidly by a vacuolar H⁺-ATPase that was detected by immunoblotting. Except for the loss of cytoskeletal proteins, few other changes over time were noted in the protein profiles of phagosomes, suggesting that phagosome maturation was incomplete. The indigestibility of the beads possibly inhibited further endocytic processing, which has been observed by others. Since nascent phagosomes contained molecules of both the cytoskeleton and plasma membrane, they will be useful in studies aimed at identifying specific protein associations occurring between membrane proteins and the cytoskeleton during phagocytosis.