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.

Determination of absolute stereochemistry, total synthesis, and evaluation of peptides from the myxomycete Physarum melleum.

The absolute stereochemistry of melleumin A (1) and B (2), novel peptide compounds isolated from the myxomycete Physarum melleum, was determined by synthesis of their segments and by a modified Mosher's method. Total synthesis of melleumin B (2) was achieved by a stereoselective method, which provided further evidence for all the absolute stereochemistries of melleumin B (2). The Wnt signal inhibitory activities of 2 and its 10R-epimer 19 were evaluated. Compound 19 showed moderate inhibition of Wnt signal transcription, which suggests that melleumin analogues might be useful as Wnt signal inhibitors.

[Isolation and characterization of the ALP1 protease from Aspergillus fumigatus and its protein inhibitor from Physarium polycephalum].

It is known that Aspergillus fumigatus secretes a serine protease ALP1 of the subtilisin family in the presence of extracellular protein substrates. We found conditions of A. fumigatus culturing that provide a high ALP1 activity inside cells without induction by extracellular proteins. The identity of the properties of the secreted and intracellular enzymes was shown. A thermostable protein inhibitor of the ALP1 protease was isolated from the plasmodium of the myxomycete Physarum polycephalum. Its molecular mass is 32-33 kDa. The inhibitor inhibits the ALP1 protease activity with IC50 of 0.14 microM. This protein was also shown to be a less efficient inhibitor of the activity of HIV-1 protease (IC50 2.5 microM). The English version of the paper: Russian Journal of Bioorganic Chemistry, 2005, vol. 31, no. 3; see also http://www.maik.ru.

Polypropionate lactones of deoxysugars glycosides from slime mold Lycogala epidendrum.

Two novel polypropionate lactone glycosides (1 and 2, i.e. lycogalinosides A and B) were isolated from the slime mold Lycogala epidendrum. Their structures, including the absolute configurations of the hydroxyl and methyls groups, were determined by means of extensive spectroscopic data such as mass, IR, UV, and 1D and 2D NMR spectra and chemical degradation followed by spectroscopic and chromatographic analysis. Compounds 1 and 2 are unique in structure containing a 2-deoxy-alpha-L-fucopyranosyl-(1-4)-6-deoxy-beta-D-gulopyranosyl unit and a beta-D-olivopyranosyl-(1-4)-beta-D-fucopyranosyl unit, respectively, and showed growth inhibitory activities against Gram-positive bacteria.

Transcription and RNA editing in a soluble in vitro system from Physarum mitochondria.

The dissection of RNA editing mechanisms in PHYSARUM: mitochondria has been hindered by the absence of a soluble in vitro system. Based on our studies in isolated mitochondria, insertion of non-encoded nucleotides into PHYSARUM: mitochondrial RNAs is closely linked to transcription. Here we have fractionated mitochondrial lysates, enriching for run-on RNA synthesis, and find that editing activity co-fractionates with pre-formed transcription elongation complexes. The establishment of this soluble transcription-editing system allows access to the components of the editing machinery and permits manipulation of transcription and editing substrates. Thus, the availability of this system provides, for the first time, a means of investigating roles for cis-acting elements, trans-acting factors and nucleotide requirements for the insertion of non-encoded nucleotides into PHYSARUM: mitochondrial RNAs. This methodology should also be broadly applicable to the study of RNA processing and editing mechanisms in a wide range of mitochondrial systems.

Calcium binding properties of recombinant calcium binding protein 40, a major calcium binding protein of lower eukaryote Physarum polycephalum.

Calcium binding protein 40 (CBP40) is a Ca(2+)-binding protein abundant in the plasmodia of Physarum polycephalum. CBP40 consists four EF-hand domains in the COOH-terminal half and a putative alpha-helix domain in the NH(2)-terminal half. We expressed recombinant proteins of CBP40 in Escherichia coli to investigate its Ca(2+)-binding properties. Recombinant proteins of CBP40 bound 4 mol of Ca(2+) with much higher affinity (pCa(1/2) = 6.5) than that of calmodulin. When residues 1-196 of the alpha-helix domain were deleted, the affinity for Ca(2+) decreased to pCa(1/2) = 4.6. A chimeric calmodulin was generated by conjugating the alpha-helix domain of CBP40 with calmodulin. The affinity of Ca(2+) for the chimeric calmodulin was higher than that for calmodulin, suggesting that the alpha-helix domain is responsible for the high affinity of CBP40 for Ca(2+). CBP40 forms large aggregates reversibly in a Ca(2+)-dependent manner. A mutant protein with a deletion of NH(2)-terminal 32 residues, however, could not aggregate, indicating the importance of these residues for the aggregation. The aggregation occurs above micromolar levels of Ca(2+) concentration, so it may only occur when CBP40 is secreted out of the plasmodial cells.

Molecular analysis of Physarum haemagglutinin I: lack of a signal sequence, sulphur amino acids and post-translational modifications.

The cDNAs encoding haemagglutinin I from plasmodia of Physarum polycephalum have been cloned using PCR protocols. The composite haemagglutinin I cDNA sequence, derived from several overlapping clones from PCR fragments, spans 408 nt and the 315 bp ORF encodes a polypeptide of 104 aa without a typical signal sequence. The putative molecular mass deduced from the amino acid sequence (10,760.76 Da) corresponds exactly to that determined by electrospray ionization MS (10,759.86 +/- 0.15 Da), suggesting that haemagglutinin I is not subject to post-translational modification. Haemagglutinin I lacks sulphur amino acids and has a beta-sheet as the major secondary structure. Expression of the coding sequence in Escherichia coli yielded a product that exhibits the same sugar-binding specificity as natural haemagglutinin I. The deduced amino acid sequence shows little similarity to that of any known lectins and thus apparently represents a novel type of lectin.

Protrusion of cell surface coupled with single exocytotic events of secretion of the slime in Physarum plasmodia.

Exocytosis has been proposed to participate in the formation of pseudopods. Using video-enhanced microscopy, we directly visualized exocytosis of single vesicles in living Physarum plasmodia migrating on a substrate. Vesicles containing slime, the plasmodial extracellular matrix, of approximately 3.5 microm in diameter, shrank at the cell periphery at the average rate of approximately 1 microm/second, and became invisible. Immediately after exocytotic events, the neighboring cell surface extended to form a protrusion. The rate of extension was approximately 1 microm/second. The protrusion showed lamella-like morphology, and contained actin microfilaments. Electron microscopy suggested that the organization of microfilaments in such protrusions may be a random meshwork rather than straight bundles. These morphologies suggest that protruded regions are pseudopods. Importantly, only the slime-containing vesicle preferentially invaded the hyaline layer that consists of dense actin microfilaments while the other vesicular organelles remained in the granuloplasm. Quantitative analysis demonstrated a linear relationship in terms of their surface area, between individual protrusions and single slime-containing vesicles. It is, therefore, likely that most of the plasma membrane of the protrusion was supplied by fusion of the slime-containing vesicle during exocytosis.

Oligomerization state in solution of the cell cycle regulators p13suc1 from the fission yeast and p9cksphy from the myxomycete Physarum, two members of the cks family.

The cks proteins (for cdc2 kinase subunit) are essential cell cycle regulators. They interact strongly with the mitotic cdc2 kinase, but the mechanism and the biological function of this association still await understanding. The oligomerization state in solution of two members of this ubiquitous protein family, the suc1 gene product from the fission yeast and the newly cloned cksphy gene product from the myxomycete Physarum, was investigated by small-angle X-ray scattering (SAXS) and biochemical methods. We found that the major molecular species are monodispersed monomeric proteins. Minor amounts of dimeric suc1 proteins were also found, but no equilibrium between the two forms was observed and surprisingly, the hexameric assemblies observed in the crystal structure of the human ckshs2 homolog were not detected. These apparent discrepancies between proteins that display cross-complementation address the question of the control of the cks oligomerization process and its link to the biological function.

Identification of proteins immunologically related to vertebrate lamins in the nuclear matrix of the myxomycete Physarum polycephalum.

Lamin-like proteins have been identified as components of the nuclear matrix of the myxomycete Physarum polycephalum. A 67 kDa homologue was detected by immunoblotting of nuclear matrix proteins with affinity-purified anti-lamin antibodies of human autoimmune sera. A 65 kDa lamin B homologue was identified with polyclonal antibodies against turkey erythrocyte lamin B in nuclei and nuclear matrix of Physarum amoebae and plasmodia. Indirect immunofluorescence microscopy revealed that the 65 and 67 kDa proteins are localized in the nuclear lamina of plasmodial nuclei.

Physarum vitronectin-like protein: an Arg-Gly-Asp-dependent cell-spreading protein with a distinct NH2-terminal sequence.

A 70-kDa protein cross-reacted with anti-bovine vitronectin was isolated from slime mold Physarum polycephalum. The NH2-terminal amino acid sequence of the protein, referred to as Physarum vitronectin-like protein, did not share any homology with those of animal vitronectins. It had cell-spreading activity, which was specifically inhibited by an Arg-Gly-Asp (RGD)-containing peptide.

F-actin bundling protein from Physarum polycephalum: purification and its capacity for co-bundling of actin filaments and microtubules.

An F-actin bundling protein was isolated and purified from plasmodium of Physarum polycephalum. The F-actin bundling protein in Physarum extract was passed through a DEAE-cellulose column. After the protein in the fraction was treated with 6 M urea, it was purified by gel filtration on Sephacryl S-300 HR followed by chromatography on CM-Toyopearl (cation exchange) in the presence of 6 M urea. The purified protein gave a single band on SDS-PAGE, and the molecular weight was estimated to be 52,000. This F-actin bundling protein is referred to as the 52 kDa protein. Interestingly, the 52 kDa protein also induced bundling of microtubules. The formation of F-actin and microtubule bundles was Ca(2+)-insensitive, but depended on the salt concentration. Each bundle formed at NaCl concentrations less than 0.1 M. The 52 kDa protein cross-reacted with monoclonal antibody raised against a HeLa 55 kDa protein (an F-actin bundling protein from HeLa cells) (Yamashiro-Matsumura and Matsumura: J. Biol. Chem. 260:5087-5097, 1985). When the 52 kDa protein was added to a mixture of actin filaments and microtubules, co-bundles composed of both filaments formed. This is the first reported example in which an F-actin bundling protein induced co-bundling of actin filaments and microtubules.

Fragmin induces tension reduction of actomyosin threads in the presence of micromolar levels of Ca2+.

Fragmin was able to reduce the isometric tension of Physarum actomyosin threads to 15-30% of the control tension at the Ca2+ concentrations greater than 10(-6) M. However, fragmin had no effect on the tension of threads when the Ca2+ concentration was lowered below 10(-7) M. The tension once reduced by fragmin could not be recovered by the removal of Ca2+. The remaining tension was shown to be still active from the experiment with quick release or stretch of the thread. This tension reduction is parallel to the decrease in viscosity of F-actin solution by fragmin. Electron microscopy showed that F-actin filaments became shorter in the thread after the tension was reduced by fragmin. Therefore, the severing of F-actin by fragmin in micromolar concentration of calcium resulted in the relaxation of tension by actomyosin threads.