The life cycles of two species of Myxomycetes in Physarales, Physarum rigidum and Didymium squamulosum.

Myxomycetes are eukaryotic microorganisms containing characteristics akin to both fungi and amoebae. They can complete their whole life cycles while being cultured on agar media, and under-laboratory conditions, which favors taxonomic, phylogenetic, and cytological researches. Here, we describe the life cycles of two such species: Didymium squamulosum collected from the field and Physarum rigidum cultured from moist chamber both belonging to the Order Physarales. Three per cent oat-agar media (OAM) was used to culture the plasmodia until they aggregated and were almost starved. Natural light was then applied to the plasmodia to induce fructification. Their life cycles share the same common stages, namely: spore, myxamoebae, swarm cell, plasmodia, and sporulation. In this study, we describe the morphogenesis from spore to spore of two species by differential interference contrast (DIC) and stereoscopic microscopies, as well as discuss the differences between the development of both species and interspecies. We found that the spore germination method of both species was the same. However, there were differences noted in time taken and fruiting body formation. Unlike P. rigidum, the species D. squamulosum did not require natural light stimulation. Moreover, the maturation process of both species had similar color transitions but exhibited distinct morphology in each developmental stage except during the swarm cell stage.

The Life Cycle of Didymium laxifilum and Physarum album on Oat Agar Culture.

The plasmodial slime molds is the largest group in the phylum Amoebozoa. Its life cycle includes the plasmodial trophic stage and the spore-bearing fruiting bodies. However, only a few species have their complete life cycle known in details so far. This study is the first reporting the morphogenesis of Didymium laxifilum and Physarum album. Spores, from field-collected sporangia, were incubated into hanging drop cultures for viewing germination and axenic oat agar plates for viewing plasmodial development and sporulation. The spores of D. laxifilum and P. album germinated by method of V-shape split and minute pore, respectively. The amoeboflagellates, released from spores, were observed in water film. The phaneroplasmodia of two species developed into a number of sporangia by subhypothallic type on oat agar culture. The main interspecific difference of morphogenesis was also discussed.

Description, culture and phylogenetic position of a new xerotolerant species of Physarum.

A new widespread myxomycete species, Physarum pseudonotabile, inhabiting the arid regions of the Eurasia, South and North America is described and illustrated. Tentatively assigned to Ph. notabile T. Macbr., a phylogeny based on the small ribosomal subunit (SSU) and elongation factor 1 alpha (EF1a) genes placed the new species in a clade far from Ph. notabile. Ph. pseudonotabile was found to be frequent in surveys based on the moist chamber culture technique with samples of litter, bark and herbivore dung collected in dry steppe and deserts of the Caspian lowland (Russia), Kazakhstan, Mongolia, China, Spain, Argentina and USA. The main morphological difference between Ph. pseudonotabile and Ph. notabile lies in spore ornamentation. Spores of the former species display irregularly distributed verrucae, whereas the latter species possesses spores with dense and regularly arranged spinulae. In addition, the ecological preferences of the two species differ. Ph. pseudonotabile inhabits the bark of living plants and ground litter in arid regions, whereas Ph. notabile is found on coarse woody debris in boreal and temperate forests. Although the new species appears to be closest to Ph. notabile morphologically, the phylogenetic analysis reveals Ph. pusillum and Ph. nivale as the closest relatives. In addition, the molecular investigations revealed a considerable amount of hidden diversity within species of Physarum with gray lime flakes. Currently we have only sufficient material to assess the morphological variation of Ph. pseudonotabile but expect that more taxa within this clade may emerge within studies combining morphological and molecular analyses.

Physarum andinum, a new nivicolous species of myxomycete from the Patagonian Andes.

A new nivicolous species of Physarum was discovered during the study of myxomycetes in the Patagonian Andes of South America. It is described herein under the name Physarum andinum. The species is characterized by stalked sporophores or more rarely sessile sporocarps or short plasmodiocarps. The sporocarps are strikingly large, reaching 2.6 mm tall and 3 mm diam when open, and have a peridium with three layers, the internal layer being clearly visible and opening separately. Physarum andinum was found at five localities in Argentina as well as in herbarium material collected about 100 y ago in Chile. The new species is reminiscent of the non-nivicolous species Physarum brunneolum, but the latter forms smaller sporophores, has darker spores and the three layers of the peridium are adhered and open together. The characters of the new species were examined under stereomicroscope, light microscope and scanning electron microscope and micrographs of relevant details are included.

Elemental composition of Physarum compressum Alb. et Schw. sporocarps and their structures cultivated on rabbit dung and agar substrates.

The elemental composition of spores, peridium walls, and lime nodes of Physarum compressum sporocarps, cultivated on rabbit dung as a natural growing environment for the slime mold and on artificial agar medium, was compared to evaluate differences that may be dependent on substrates. Whole fruiting bodies and samples of both experimental media were extracted with nitric acid or Parr digest bomb, respectively, and analyzed by means of total X-ray reflection fluorescence (TXRF). Electron probe microanalysis (EPMA) of spores, peridium walls, and lime nodes structure was carried out with the scanning electron microscope equipped with energy-dispersive spectrometer. Because of minute sizes and roughness of investigated structures, Monte Carlo simulations were utilized to establish analytical conditions of EPMA. Biological and geological standards were used in the quantification of element concentrations. According to TXRF, the fruiting bodies from agar medium revealed lower concentrations of K, Ca, Cr, Mn, and Fe in relation to fruiting bodies from the dung, reflecting elemental relationships in the experimental media. According to EPMA, the highest Ca concentration was found in the lime nodes followed by the peridium and the spores. Culturing of the slime molds on the rabbit dung indicated higher concentration of Ca in the lime nodes and peridium walls when compared with those obtained from the sporocarps grown on agar media. The opposite relation was found for the spores. The concentration of Na, Mg, P, S, and Cl was generally lower in all structures of the sporocarps harvested from the dung than from the agar medium. K was in higher concentration in analyzed structures from dung than from agar. Different element uptake (except for Ca and K) was revealed by the two methods: TXRF and EPMA.

A model of network formation by Physarum plasmodium: interplay between cell mobility and morphogenesis.

The plasmodium of Physarum polycephalum has attracted much attention due its intelligent adaptive behavior. In this study, we constructed a model of the organism and attempted to simulate its locomotion and morphogenetic behavior. By modifying our previous model, we were able to get closer to the actual behavior. We also compared the behavior of the model with that of the real organism, demonstrating remarkable similarity between the two.

Spore-to-spore agar culture of the myxomycete Physarum globuliferum.

The ontogeny of the myxomycete Physarum globuliferum was observed on corn meal agar and hanging drop cultures without adding sterile oat flakes, bacteria or other microorganisms. Its complete life cycle including spore germination, myxamoebae, swarm cells, plasmodial development, and maturity of fructifications was demonstrated. Details of spore-to-spore development are described and illustrated.

Physarum machines: encapsulating reaction-diffusion to compute spanning tree.

The Physarum machine is a biological computing device, which employs plasmodium of Physarum polycephalum as an unconventional computing substrate. A reaction-diffusion computer is a chemical computing device that computes by propagating diffusive or excitation wave fronts. Reaction-diffusion computers, despite being computationally universal machines, are unable to construct certain classes of proximity graphs without the assistance of an external computing device. I demonstrate that the problem can be solved if the reaction-diffusion system is enclosed in a membrane with few 'growth points', sites guiding the pattern propagation. Experimental approximation of spanning trees by P. polycephalum slime mold demonstrates the feasibility of the approach. Findings provided advance theory of reaction-diffusion computation by enriching it with ideas of slime mold computation.

First report of sporangia of a myxomycete (Physarum pusillum) on the body of a living animal, the lizard Corytophanes cristatus.

Myxomycetes are protists whose life cycle depends on aerially dispersed spores that germinate into motile myxamoebae, which then pair and fuse to form a larger, motile plasmodium. The plasmodium seeks out a suitable fruiting site (usually atop vegetative material or detritus) and transforms into fruiting bodies that release the spores. In this paper we report the first known instance of a myxomycete, in this case Physarum pusillum, sporulating on the body of a living animal, the cryptic lizard Corytophanes cristatus, which was collected in eastern Honduras in 2003.

Involvement of actin dephosphorylation in germination of Physarum sclerotium.

The plasmodium of Physarum polycephalum grows without cytokinesis and shows an active cytoplasmic streaming under wet and nutritious conditions. It can undergo reversible differentiation into several types of dormancy to survive in adverse environments. Temperature change or osmotic stress leads to cytoplasmic division of the plasmodium into cells containing one or more nuclei: these form a macrocyst, the spherule. Desiccation also induces cell division of the plasmodium followed by formation of a sclerotium, a dormant body resistant to dry stress. More than half of the actin in a sclerotium is phosphorylated at a single site, threonine 203, resulting in loss of its ability to polymerize into actin filaments. In the present study, actin phosphorylation was found in the sclerotium but not in either the plasmodium or in the spherule. This result suggests that phosphorylation of sclerotium actin may be related to the mechanism associated with desiccation resistance rather than morphological changes through cell compartmentalization in the macrocyst formation. Moreover. dephosphorylation of the phosphorylated form of sclerotium actin began within 5 min after addition of water. Dephosphorylation was not affected by sucrose and sorbitol sugars, but was inhibited by ammonium bicarbonate, ammonium phosphate, sodium phosphate, NaCl, and KCl in a dose-dependent manner. On the other hand, in germination of the sclerotium there was measurable sensitivity to both carbohydrates and salts. Actin dephosphorylation seems to be one of the important processes in the early phase of sclerotium germination.

Smart behavior of true slime mold in a labyrinth.

Even for humans it is not easy to solve a maze. But the plasmodium of true slime mold, an amoeba-like unicellular organism, has shown an amazing ability to do so. This implies that an algorithm and a high computing capacity are included in the unicellular organism. In this report, we discuss information processing in the microorganism to focus on the issue as to whether the maze-solving behavior is akin to primitive intelligence.

Condensation-decondensation of the gamma-tubulin containing material in the absence of a structurally visible organelle during the cell cycle of Physarum plasmodia.

Genetic evidence has shown the presence of a common spindle pole organiser in Physarum amoebae and plasmodia. But the typical centrosome and mitosis observed in amoebae are replaced in plasmodia by an intranuclear mitosis devoid of any structurally defined organelle. The fate of gamma-tubulin and of another component (TPH17) of the centrosome of Physarum amoebae was investigated in the nuclei of synchronous plasmodia. These two amoebal centrosomal elements were present in the nuclear compartment during the entire cell cycle and exhibited similar relocalisation from metaphase to telophase. Three preparation methods showed that gamma-tubulin containing material was dispersed in the nucleoplasm during interphase. It constituted an intranuclear thread-like structure. In contrast, the TPH17 epitope exhibited a localisation close to the nucleolus. In late G2-phase, the gamma-tubulin containing elements condensed in a single organelle which further divided. Intranuclear microtubules appeared before the condensation of the gamma-tubulin material and treatment with microtubule poisons suggested that microtubules were required in this process. The TPH17 epitope relocalised in the intranuclear spindle later than the gamma-tubulin containing material suggesting a maturation process of the mitotic poles. The decondensation of the gamma-tubulin material and of the material containing the TPH17 epitope occurred immediately after telophase. Hence in the absence of a structurally defined centrosome homologue, the microtubule nucleating material undergoes a cycle of condensation and decondensation during the cell cycle.

Preferential expression of one beta-tubulin gene during flagellate development in Physarum.

The microbial eukaryote Physarum polycephalum displays several distinct cell types in its life cycle, including amoebae, flagellates and plasmodia. Despite its relative simplicity, Physarum has a tubulin gene family of complexity comparable to that of Drosophila. We have identified beta-tubulin cDNAs from Physarum that are derived from the betA beta-tubulin locus and encode beta 1A tubulin. We have also identified a partial cDNA for the unlinked betB beta-tubulin gene, which encodes beta 1B tubulin. The polypeptide sequences encoded by betA and betB show 99% identity, but the nucleotide sequences show only 85% identity, consistent with an ancient duplication of these genes. The betB gene is expressed in amoebae, flagellates and plasmodia, whereas betA is expressed only in amoebae and flagellates. During the amoeba-flagellate transition the level of betA transcript increases over 100-fold, while the level of betB transcript changes very little. Thus Physarum has a mechanism for regulating the level of discrete beta-tubulin transcripts differentially during flagellate development. A need for this differential regulation could account for the maintenance of the virtually isocoding betA and betB beta-tubulin genes.

Isolation, characterisation and growth-related changes of an HMG-like protein from microplasmodia of Physarum polycephalum.

An alanine, lysine and glutamic acid-rich nuclear protein (P2) of Mr approximately 19,500 co-extracts with the histones from nuclei of Physarum polycephalum when using the CaCl2 method for histone extraction [1] and was found to have the composition previously ascribed to a putative histone H1(0) isolated from microplasmodia using 5% PCA (Yasuda, H., Mueller, R.D., Logan, K.A. and Bradbury, E.M. (1986) J. Biol. Chem. 261, 2349-2354). P2 has very similar electrophoretic properties to chicken erythrocyte histone H5, calf thymus histone H1(0) and the Physarum HMG-like protein AS-2, but does not appear to be immunologically or structurally similar to H5 or H1(0). An increase in the abundance of P2 was observed during exponential growth in microplasmodia, reaching an approximately 1:1 ratio with histone H1 by 48 h of culture. Standard amino acid analysis and NMR show that P2 is more HMG-like than H1-like and CD measurements demonstrated that P2 contains only 5% secondary structure in its maximally structured state and is, therefore, essentially unstructured under in vivo conditions. Also possible clustering of acidic residues is detected using CD and may be of functional significance. Analysis of post-translational modification of P2 shows that it is phosphorylated at up to three sites as isolated from immature spherules. The relationship of P2 to the HMG family of proteins and AS-2 is discussed.

Genetic analysis of the relationships between the amoebal extranuclear spindle-organizing centre and the plasmodial intranuclear spindle-organizing centre of Physarum during conjugation.

Physarum amoebae possess an extranuclear spindle-organizing centre (abbreviated SPOC), located in a typical centrosome with a pair of associated centrioles while plasmodia possess an intranuclear SPOC without centrioles. In order to ascertain whether, during conjugation, the plasmodial SPOC is derived from the amoebal one or is not related to it, we have constructed amoebal strains possessing two and three SPOCs and we have used as a genetic marker the frequency of polycentric metaphases in order to evaluate the number of SPOCs in the plasmodia. The results of both symmetrical crosses, i.e. between amoebae possessing the same number of SPOCs, and asymmetrical crosses, i.e. between amoebae possessing a different number of SPOCs, show that: (1) the number of SPOCs in plasmodia is dependent upon the number of SPOCs in either one of the two parental amoeba; (2) in no cross does the number of plasmodial SPOCs equal the sum of the parental amoebal SPOCs, but it corresponds to that of only one parent without any polarity of transmission in asymmetrical crosses. These results are consistent with the following model: (1) plasmodial SPOCs are derived from the amoebal ones; and (2) one set of parental SPOCs is lost, destroyed or inactivated in the zygote.

Topoisomerase I in actively growing plasmodia and during differentiation of the slime mold Physarum polycephalum.

A type I topoisomerase has been purified from nuclei of a slime mold Physarum polycephalum and its activity was tested during spherulation. The final preparation contained a single polypeptide of about 100 kDa. Basic properties of Physarum topoisomerase I (substrate specificity, ionic requirement, sensitivity to inhibitors) were similar to those of topoisomerases from higher eukaryotes. Specific features of Physarum enzyme were that it was rapidly inactivated at 45 degrees C and did not react with antibodies against human topoisomerase I. The activity of topoisomerase I in developed dormant spherules decreased approx. 2-fold, as compared with a 4-fold decrease of RNA and a 10-fold decrease of DNA synthesis. Basic properties of the enzyme remained unchanged during spherulation.

Variable pathways for developmental changes in composition and organization of microtubules in Physarum polycephalum.

The development of uninucleate amoebae into multinucleate plasmodia in myxomycetes is called the amoebal-plasmodial transition (APT). During the APT in Physarum polycephalum the ability to form flagellar axonemes is lost; the astral, open mitosis is replaced by the anastral, closed mitosis; and cytoskeletal microtubules disappear. These changes are accompanied by alterations in the repertoire of expressed tubulins. Using immunofluorescence microscopy we have studied the timing of loss and accumulation of developmentally regulated tubulin isotypes in relation to other cellular events during the APT. We specifically asked whether changes in the composition of microtubules are correlated with changes in their organization. The plasmodium-specific beta 2-tubulin can first be detected in microtubules of uninucleate cells after they become committed to plasmodium formation. However, rare cells are observed that exhibit beta 2-tubulin at earlier or only at later stages of development. Amoeba-specific acetylated alpha 3-tubulin disappears gradually during development. Individual cells differ in the timing of loss of this isotype: alpha 3-tubulin is present in the majority of uninucleate cells, in a fraction of binucleate and quadrinucleate cells, and is absent from larger multinucleate cells. Cytoplasmic microtubules in uninucleate cells are organized by a single microtubule-organizing center (MTOC) juxtaposed to the nucleus. Binucleate cells and quadrinucleate cells exhibit variable numbers of MTOCs. Cytoplasmic microtubules persist during the APT until the stage of plasmodia containing at least 100 nuclei. The lack of a strict correlation between the changes in tubulin composition and changes in organization of microtubular structures indicates that accumulation of beta 2-tubulin and disappearance of alpha 3-tubulin isotypes are not sufficient to bring about reorganization of microtubules during development. Individual cells in a developing population differ not only in the succession of accumulation and loss of developmentally regulated tubulins, but also in the sequences of other cellular changes occurring during the APT.

Acid-soluble purine and pyrimidine derivatives of growing, encysting and encystment-inhibited amoebae.

The intracellular acid-soluble purine and pyrimidine derivatives of myxamoebae-swarm cells of Physarum flavicomum were investigated during growth, microcyst formation, and during adenine-inhibition of encystment, using high performance liquid chromatography (HPLC). We also studied the incorporation of exogenous radioactive adenine into the acid soluble purine derivatives and S-adenosyl-sulphur compounds separated by HPLC. The most abundant ribonucleoside monophosphate was AMP in the growing and 15 h encysting cells (NC), while it was UMP in the 15 h adenine-inhibited cells (AIC). ADP was the nucleoside diphosphate present in the greatest quantity in the growing and NC cells but it was CDP in the AIC. The nucleoside triphosphate in highest concentration was ATP, UTP, and GTP in growing, NC, and AIC, respectively. Guanosine was the most abundant nucleoside in all cells. The nucleobase occurring in greatest concentration was cytosine, cytosine and guanine, and adenine in the growing, NC, and AIC, respectively. The AMP content in the 15 h AIC was 2.1-fold higher than that of adenosine. The 15 h NC had the lowest adenylate energy charge, a value of 0.54 +/- 0.02, while the values for growing cells and the AIC were 0.62 +/- 0.02 and 0.76 +/- 0.01, respectively. [14C]-Adenine labelling studies (15 h) revealed the occurrence of purine nucleotide interconversion, as the label was detected not only in adenosine, AMP, ADP, ATP, but also in guanine, guanosine, GMP, GDP, GTP, as well as, in inosine monophosphate and xanthosine monophosphate. The percentage incorporation of the radiolabelled adenine into AMP was higher than into adenosine. An increased intracellular level of guanine nucleotides is associated with the inhibition of encystment. The extracellular adenine, rather than internal adenine sources, appears to be the primary precursor of nucleotide for S-adenosylmethionine synthesis during adenine-inhibition of encystment.

DNA methylation pattern during the encystment of Physarum flavicomum.

In Physarum flavicomum Berk., haploid myxamoebae convert to dormant microcysts under conditions of nutrient imbalance. Exogenous adenine increases the intracellular content of S-adenosylmethionine (SAM) and inhibits this process. However, treatments that reduce the intracellular SAM levels relieve the inhibition of encystment induced by adenine. SAM plays a major metabolic role in cellular transmethylation reactions. In this study, we compared the DNA methylation patterns of growing cells, encysting cells, adenine-inhibited cells, and cysts using three different approaches: incubation of the cells with [14C]methylmethionine and detection of the labeled methyl group in purified DNA samples; analyses of DNA base composition by high performance liquid chromatography; and restriction endonuclease analyses of DNA. We found that DNA from the adenine-treated cells was labelled 1.3 times more with [14C]methylmethionine than was the DNA of untreated encysting cells. The DNA G + C content of this species was about 41%. The DNA of growing cells had the highest 5-methylcytosine (5MC) content, while DNA from the cysts had the lowest (about 27% that of growing cells). Adenine-inhibited cells had about 1.2 times more DNA-5MC than did encysting cells. Using the restriction enzymes SmaI, PvuI, and XhoI (which are inhibited by C residue methylation), we found that cyst DNA had more cutting sites than did amoebal DNA. By using the restriction enzyme DpnI which cuts DNA at GmATC sites, we found that cyst DNA, but not growing cell DNA, contained N6-methyladenine.

Differential synthesis of histone H1 during early spherulation in Physarum polycephalum.

H1 and P2 (an H1 degree/HMG-like protein) accumulate during exponential growth of Physarum microplasmodia (unpublished results), indicating that these proteins may play a role in differentiation (spherulation). To test this hypothesis, pulse labelling using [14C]lysine was used to determine whether any differential histone synthesis occurs during salts-induced spherulation. A peak in the uptake of [14C]lysine into microplasmodia was detected between 12 and 24 h following salts-induction. During the same interval, incorporation of label into the CaCl2-extracted histones occurred, with H1 being synthesised at approx. 3 times the level of the core histones and P2. Densitometry of SDS-PAGE gels showed that high levels of H1 were maintained up to 40 h in salts medium, beyond the observed peak in synthesis. The synthesis and accumulation of high levels of H1 during early spherulation indicates a role for this histone in the initiation and maintenance of a transcriptionally inactive differentiated state.