Characterization of chitinases from the GH18 gene family in the myxomycete Physarum polycephalum.

BACKGROUND: Physarum polycephalum is an unusual macroscopic myxomycete expressing a large range of glycosyl hydrolases. Among them, enzymes from the GH18 family can hydrolyze chitin, an important structural component of the cell walls in fungi and in the exoskeleton of insects and crustaceans. METHODS: Low stringency sequence signature search in transcriptomes was used to identify GH18 sequences related to chitinases. Identified sequences were expressed in E. coli and corresponding structures modelled. Synthetic substrates and in some cases colloidal chitin were used to characterize activities. RESULTS: Catalytically functional hits were sorted and their predicted structures compared. All share the TIM barrel structure of the GH18 chitinase catalytic domain, optionally fused to binding motifs, such as CBM50, CBM18, and CBM14, involved in sugar recognition. Assessment of the enzymatic activities following deletion of the C-terminal CBM14 domain of the most active clone evidenced a significant contribution of this extension to the chitinase activity. A classification based on module organization, functional and structural criteria of characterized enzymes was proposed. CONCLUSIONS: Physarum polycephalum sequences encompassing a chitinase like GH18 signature share a modular structure involving a structurally conserved catalytic TIM barrels decorated or not by a chitin insertion domain and optionally surrounded by additional sugar binding domains. One of them plays a clear role in enhancing activities toward natural chitin. GENERAL SIGNIFICANCE: Myxomycete enzymes are currently poorly characterized and constitute a potential source for new catalysts. Among them glycosyl hydrolases have a strong potential for valorization of industrial waste as well as in therapeutic field.

The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum.

The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone chaperones. They escort histones during their entire cellular life and ensure their proper incorporation in chromatin. Physarum polycephalum is a Mycetozoan, a clade located at the crown of the eukaryotic tree. We previously found that histones, which are highly conserved between plants and animals, are also highly conserved in Physarum. However, histone chaperones differ significantly between animal and plant kingdoms, and this thus probed us to further study the conservation of histone chaperones in Physarum and their evolution relative to animal and plants. Most of the known histone chaperones and their functional domains are conserved as well as key residues required for histone and chaperone interactions. Physarum is divergent from yeast, plants and animals, but PpHIRA, PpCABIN1 and PpSPT6 are similar in structure to plant orthologues. PpFACT is closely related to the yeast complex, and the Physarum genome encodes the animal-specific APFL chaperone. Furthermore, we performed RNA sequencing to monitor chaperone expression during the cell cycle and uncovered two distinct patterns during S-phase. In summary, our study demonstrates the conserved role of histone chaperones in handling histones in an early-branching eukaryote.

Usage of the H3 variants during the S-phase of the cell cycle in Physarum polycephalum.

DNA replication occurring in S-phase is critical for the maintenance of the cell fate from one generation to the next, and requires the duplication of epigenetic information. The integrity of the epigenome is, in part, insured by the recycling of parental histones and de novo deposition of newly synthesized histones. While the histone variants have revealed important functions in epigenetic regulations, the deposition in chromatin during S-phase of newly synthesized histone variants remains unclear. The identification of histone variants of H3 and unique features of Physarum polycephalum provides a powerful system for investigating de novo deposition of newly synthesized histones by tracking the incorporation of exogenous histones within cells. The analyses revealed that the rate of deposition of H3.1 and H3.3 is anticorrelated as S-phase progresses, H3.3 is predominately produced and utilized in early S and dropped throughout S-phase, while H3.1 behaved in the opposite way. Disturbing the expression of H3 variants by siRNAs revealed mutual compensation of histone transcripts. Interestingly, the incorporation of pre-formed constrained histone complexes showed that tetramers of H3/H4 are more efficiently utilized by the cell than dimers. These results support the model whereby the histone variant distribution is established upon replication and new histone deposition.

Semi-in vitro detection of Mg2+-dependent DNase that specifically digest mitochondrial nucleoids in the zygote of Physarum polycephalum.

The maternal/uniparental inheritance of mitochondria is controlled by the selective elimination of paternal/uniparental mitochondria and digestion of their mitochondrial DNA (mtDNA). In isogamy, the selective digestion of mtDNA in uniparental mitochondria is initiated after mating and is completed prior to the elimination of mitochondria, but the molecular mechanism of the digestion of uniparental mtDNA remains unknown. In this study, we developed a semi-in vitro assay for DNase, wherein the digestion of mitochondrial nucleoids (mt-nucleoids) was microscopically observed using isolated mitochondria from Physarum polycephalum and the DNase involved in uniparental inheritance was characterized. When myxamoebae of AI35 and DP246 are crossed, mtDNA and mt-nucleoid from only the DP246 parent are digested. The digestion of mt-nucleoids was observed in zygotes 3 h after plating for mating. During the digestion of mt-nucleoids, mitochondrial membrane integrity was maintained. In the semi-in vitro assay, the digestion of mt-nucleoids was only observed in the presence of Mg2+ at pH 7.5-9.0. Moreover, such Mg2+-dependent DNase activity was specifically detected in mitochondria isolated from zygotes 3 h after plating for mating. Therefore, Mg2+-dependent DNase is potentially involved in uniparental inheritance. Our findings provide insights into the DNase involved in uniparental inheritance and its regulatory mechanism.

Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium.

In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic protists such as slime molds generate diverse and complex structures while remaining in a multinucleate syncytial state. It is unknown if different regions of these giant syncytial cells have distinct transcriptional responses to environmental encounters and if nuclei within the cell diversify into heterogeneous states. Here, we performed spatial transcriptome analysis of the slime mold Physarum polycephalum in the plasmodium state under different environmental conditions and used single-nucleus RNA-sequencing to dissect gene expression heterogeneity among nuclei. Our data identifies transcriptome regionality in the organism that associates with proliferation, syncytial substructures, and localized environmental conditions. Further, we find that nuclei are heterogenous in their transcriptional profile and may process local signals within the plasmodium to coordinate cell growth, metabolism, and reproduction. To understand how nuclei variation within the syncytium compares to heterogeneity in single-nucleus cells, we analyzed states in single Physarum amoebal cells. We observed amoebal cell states at different stages of mitosis and meiosis, and identified cytokinetic features that are specific to nuclei divisions within the syncytium. Notably, we do not find evidence for predefined transcriptomic states in the amoebae that are observed in the syncytium. Our data shows that a single-celled slime mold can control its gene expression in a region-specific manner while lacking cellular compartmentalization and suggests that nuclei are mobile processors facilitating local specialized functions. More broadly, slime molds offer the extraordinary opportunity to explore how organisms can evolve regulatory mechanisms to divide labor, specialize, balance competition with cooperation, and perform other foundational principles that govern the logic of life.

Cytotoxicity activities and chemical characteristics of exopolysaccharides and intracellular polysaccharides of Physarum polycephalum microplasmodia.

BACKGROUND: Microbial polysaccharides have been reported to possess remarkable bioactivities. Physarum polycephalum is a species of slime mold for which the microplasmodia are capable of rapid growth and can produce a significant amount of cell wall-less biomass. There has been a limited understanding of the polysaccharides produced by microplasmodia of slime molds, including P. polycephalum. Thus, the primary objectives of this research were first to chemically characterize the exopolysaccharides (EPS) and intracellular polysaccharides (IPS) of P. polycephalum microplasmodia and then to evaluate their cytotoxicity against several cancer cell lines. RESULTS: The yields of the crude EPS (4.43 ± 0.44 g/l) and partially purified (deproteinated) EPS (2.95 ± 0.85 g/l) were comparable (p > 0.05) with the respective crude IPS (3.46 ± 0.36 g/l) and partially purified IPS (2.45 ± 0.36 g/l). The average molecular weight of the EPS and IPS were 14,762 kDa and 1788 kDa. The major monomer of the EPS was galactose (80.22%), while that of the IPS was glucose (84.46%). Both crude and purified IPS samples showed significantly higher cytotoxicity toward Hela cells, especially the purified sample and none of the IPSs inhibited normal cells. Only 38.42 ± 2.84% Hela cells remained viable when treated with the partially purified IPS (1 mg/ml). However, although only 34.76 ± 6.58% MCF-7 cells were viable when exposed to the crude IPS, but the partially purified IPS displayed non-toxicity to MCF-7 cells. This suggested that the cytotoxicity toward MCF-7 would come from some component associated with the crude IPS sample (e.g. proteins, peptides or ion metals) and the purification process would have either completely removed or reduced amount of that component. Cell cycle analysis by flow cytometry suggested that the mechanism of the toxicity of the crude IPS toward MCF-7 and the partially purified IPS toward Hela cells was due to apoptosis. CONCLUSIONS: The EPS and IPS of P. polycephalum microplasmodia had different chemical properties including carbohydrate, protein and total sulfate group contents, monosaccharide composition and molecular weights, which led to different cytotoxicity activities. The crude and partially purified IPSs would be potential materials for further study relating to cancer treatment.

Encoding memory in tube diameter hierarchy of living flow network.

The concept of memory is traditionally associated with organisms possessing a nervous system. However, even very simple organisms store information about past experiences to thrive in a complex environment-successfully exploiting nutrient sources, avoiding danger, and warding off predators. How can simple organisms encode information about their environment? We here follow how the giant unicellular slime mold Physarum polycephalum responds to a nutrient source. We find that the network-like body plan of the organism itself serves to encode the location of a nutrient source. The organism entirely consists of interlaced tubes of varying diameters. Now, we observe that these tubes grow and shrink in diameter in response to a nutrient source, thereby imprinting the nutrient's location in the tube diameter hierarchy. Combining theoretical model and experimental data, we reveal how memory is encoded: a nutrient source locally releases a softening agent that gets transported by the cytoplasmic flows within the tubular network. Tubes receiving a lot of softening agent grow in diameter at the expense of other tubes shrinking. Thereby, the tubes' capacities for flow-based transport get permanently upgraded toward the nutrient location, redirecting future decisions and migration. This demonstrates that nutrient location is stored in and retrieved from the networks' tube diameter hierarchy. Our findings explain how network-forming organisms like slime molds and fungi thrive in complex environments. We here identify a flow networks' version of associative memory-very likely of relevance for the plethora of living flow networks as well as for bioinspired design.

Effects of medium composition on the growth and lipid production of microplasmodia of Physarum polycephalum.

Physarum polycephalum is a plasmodial slime mold. One of the trophic stages in the life cycle of this organism is a plasmodium. In submerged culture, plasmodia are fragmented into microplasmodia. The latter both lack cell walls and are capable of rapid growth. There has been limited information on the effects of medium composition on the growth and lipid accumulation of microplasmodia. In this study, optimization of medium components by response surface methodology showed that tryptone and yeast extract concentrations had the most significant effects on lipid and biomass production; significant synergistic interactions between glucose and tryptone concentration on these responses were also recorded. The optimal medium was composed of 20 g/L of glucose, 6.59 g/L of tryptone, and 3.0 g/L of yeast extract. This medium yielded 13.86 g/L of dry biomass and 1.97 g/L of lipids. These amounts are threefold higher than those of the American Type Culture Collection (ATCC) medium. In addition, biomass and lipid production reached maximal values between only 4 and 5 days. Fatty acid compositions analysis by gas chromatography-mass spectrometer (GC-MS) revealed that P. polycephalum lipids consisted mainly of oleic acid (40.5%), linoleic acid (10%), and octadecynoic (15.8%). This is the first report on the fatty acid composition of P. polycephalum microplasmodia. These results suggest that the biomass of microplasmodia could be used as a source of material for direct conversion into biodiesel because of the absence of cell walls or it could also be used as a supplemental source of beneficial fatty acids for humans, albeit with some further evaluation needed.

Identification of a glutathione S-transferase gene of Physarum polycephalum as a biomarker for nanosized TiO2 exposure under dark conditions.

In this study, a glutathione S-transferase gene (gst) from sensitive Physarum polycephalum was selected for its ability to detect nanosized TiO2 (nTiO2 ) exposure under dark conditions. The concentration of nTiO2 (25, 40 and 60 nm) for subsequent assays was first determined (5-18 mg ml-1 ) and total GST enzyme activity of P. polycephalum was confirmed to be increased 6-44 fold in groups treated with nTiO2 . Second, an RNA-seq study was performed to identify candidate gst genes before isolation of an optimum gst gene of P. polycephalum (Ppgst), which encoded 223 amino acids. Third, the transcriptional level of the Ppgst gene was further confirmed to be positively correlated with nTiO2 exposure within the concentration range of (5-15 mg ml-1 ) by qPCR. In conclusion, these results indicated that the transcriptional level of Ppgst can reflect nTiO2 exposure, suggesting that it may be employed as a new biomarker for nTiO2 pollution under dark conditions. SIGNIFICANCE AND IMPACT OF THE STUDY: This study identifies a new gst gene for indicating nanosized TiO2 under dark conditions and provides a new option for detection of nanosized TiO2 pollution under dark conditions.

Nano-sized TiO2 (nTiO2) induces metabolic perturbations in Physarum polycephalum macroplasmodium to counter oxidative stress under dark conditions.

Nano-sized TiO2 (nTiO2) exerts an oxidative effect on cells upon exposure to solar or UV irradiation and ecotoxicity of the nTiO2 is an urgent concern. Little information is available regarding the effect of TiO2 on cells under dark conditions. Metabolomics is a unique approach to the discovery of biomarkers of nTiO2 cytotoxicity, and leads to the identification of perturbed metabolic pathways and the mechanism underlying nTiO2 toxicity. In the present study, gas chromatography mass spectrometry (GC/MS)-based metabolomics was performed to investigate the effect of nTiO2 on sensitive cells (P. polycephalum macroplasmodium) under dark conditions. According to the multivariate pattern recognition analysis, at least 60 potential metabolic biomarkers related to sugar metabolism, amino acid metabolism, nucleotide metabolism, polyamine biosynthesis, and secondary metabolites pathways were significantly perturbed by nTiO2. Notably, many metabolic biomarkers and pathways were related to anti-oxidant mechanisms in the living organism, suggesting that nTiO2 may induce oxidative stress, even under dark conditions. This speculation was further validated by the biochemical levels of reactive oxygen species (ROS), 8-hydroxy-2-deoxyguanosine (8-OHdG), and total soluble phenols (TSP). We inferred that the oxidative stress might be related to nTiO2-induced imbalance of cellular ROS. To the best of our knowledge, the present study is the first to investigate the nTiO2-induced metabolic perturbations in slime mold, provide a new perspective of the mechanism underlying nTiO2 toxicity under dark conditions, and show that metabolomics can be employed as a rapid, reliable and powerful tool to investigate the interaction among organisms, the environment, and nanomaterials.

A revised model of fluid transport optimization in Physarum polycephalum.

Optimization of fluid transport in the slime mold Physarum polycephalum has been the subject of several modeling efforts in recent literature. Existing models assume that the tube adaptation mechanism in P. polycephalum's tubular network is controlled by the sheer amount of fluid flow through the tubes. We put forward the hypothesis that the controlling variable may instead be the flow's pressure gradient along the tube. We carry out the stability analysis of such a revised mathematical model for a parallel-edge network, proving that the revised model supports the global flow-optimizing behavior of the slime mold for a substantially wider class of response functions compared to previous models. Simulations also suggest that the same conclusion may be valid for arbitrary network topologies.

Physarum polycephalum for Studying the Function of Histone Modifications In Vivo.

Histone modifications have been widely correlated with genetic activities. However, how these posttranslational modifications affect the dynamics and the structure of chromatin is poorly understood. Here, we describe the incorporation of the exogenous histone proteins into the slime mold Physarum polycephalum, which has been revealed to be a valuable tool for examining different facets of the function histones in chromatin dynamics like replication-coupled chromatin assembly, histone exchange, and nucleosome turnover.

Towards a Physarum learning chip.

Networks of protoplasmic tubes of organism Physarum polycehpalum are macro-scale structures which optimally span multiple food sources to avoid repellents yet maximize coverage of attractants. When data are presented by configurations of attractants and behaviour of the slime mould is tuned by a range of repellents, the organism preforms computation. It maps given data configuration into a protoplasmic network. To discover physical means of programming the slime mould computers we explore conductivity of the protoplasmic tubes; proposing that the network connectivity of protoplasmic tubes shows pathway-dependent plasticity. To demonstrate this we encourage the slime mould to span a grid of electrodes and apply AC stimuli to the network. Learning and weighted connections within a grid of electrodes is produced using negative and positive voltage stimulation of the network at desired nodes; low frequency (10 Hz) sinusoidal (0.5 V peak-to-peak) voltage increases connectivity between stimulated electrodes while decreasing connectivity elsewhere, high frequency (1000 Hz) sinusoidal (2.5 V peak-to-peak) voltage stimulation decreases network connectivity between stimulated electrodes. We corroborate in a particle model. This phenomenon may be used for computation in the same way that neural networks process information and has the potential to shed light on the dynamics of learning and information processing in non-neural metazoan somatic cell networks.

On the Computing Potential of Intracellular Vesicles.

Collision-based computing (CBC) is a form of unconventional computing in which travelling localisations represent data and conditional routing of signals determines the output state; collisions between localisations represent logical operations. We investigated patterns of Ca2+-containing vesicle distribution within a live organism, slime mould Physarum polycephalum, with confocal microscopy and observed them colliding regularly. Vesicles travel down cytoskeletal 'circuitry' and their collisions may result in reflection, fusion or annihilation. We demonstrate through experimental observations that naturally-occurring vesicle dynamics may be characterised as a computationally-universal set of Boolean logical operations and present a 'vesicle modification' of the archetypal CBC 'billiard ball model' of computation. We proceed to discuss the viability of intracellular vesicles as an unconventional computing substrate in which we delineate practical considerations for reliable vesicle 'programming' in both in vivo and in vitro vesicle computing architectures and present optimised designs for both single logical gates and combinatorial logic circuits based on cytoskeletal network conformations. The results presented here demonstrate the first characterisation of intracelluar phenomena as collision-based computing and hence the viability of biological substrates for computing.

Magnetic Nanoparticles-Loaded Physarum polycephalum: Directed Growth and Particles Distribution.

Slime mold Physarum polycephalum is a single cell visible by an unaided eye. The slime mold optimizes its network of protoplasmic tubes to minimize expose to repellents and maximize expose to attractants and to make efficient transportation of nutrients. These properties of P. polycephalum, together with simplicity of its handling and culturing, make it a priceless substrate for designing novel sensing, computing and actuating architectures in living amorphous biological substrate. We demonstrate that, by loading Physarum with magnetic particles and positioning it in a magnetic field, we can, in principle, impose analog control procedures to precisely route active growing zones of slime mold and shape topology of its protoplasmic networks.

Evaluation of Physarum polycephalum plasmodial growth and lipid production using rice bran as a carbon source.

BACKGROUND: The myxomycete Physarum polycephalum appears to have remarkable potential as a lipid source for biodiesel production. The present study evaluated the use of rice bran as a carbon source and determined the medium components for optimum growth and lipid production for this organism. RESULTS: Optimization of medium components by response surface methodology showed that rice bran and yeast extract had significant influences on lipid and biomass production. The optimum medium consisted of 37.5 g/L rice bran, 0.79 g/L yeast extract and 12.5 g/L agar, and this yielded 7.5 g/L dry biomass and 0.9 g/L lipid after 5 days. The biomass and lipid production profiles revealed that these parameters increased over time and reached their maximum values (10.5 and 1.26 g/L, respectively) after 7 days. Physarum polycephalum growth decreased on the spent medium but using the latter increased total biomass and lipid concentrations to 14.3 and 1.72 g/L, respectively. CONCLUSIONS: An effective method for inoculum preparation was developed for biomass and lipid production by P. polycephalum on a low-cost medium using rice bran as the main carbon source. These results also demonstrated the feasibility of scaling up and reusing the medium for additional biomass and lipid production.

Transfer function of protoplasmic tubes of Physarum polycephalum.

The slime mould Physarum polycephalum is a large single celled myxomycete; its plasmodium consists of tubes which extend to find sources of food. It has been previously shown that the tubes are conductive with a resistance of approximately 3 MΩ, and have been used in basic DC circuits. Hybrid slime mould-electronic circuits have been proposed, using the protoplasmic tubes, grown between agar, as Physarum wires. This paper aims to evaluate the electrical properties of the protoplasmic tubes with respect to analogue and digital waveforms. The Physarum wires act as low pass filters with a mean cut off frequency of 19kHz (SD 9 KHz); they have a 12.1 dB/decade roll-off (SD 1.9 dB/decade). Mean attenuation across the band-pass range is -6 dB (S.D. 4.5 dB). The mechanism for the frequency dependant attenuation is unknown however a combination of protoplasmic electrolyte and the cytoskeletal structure is the most likely cause. The tubes last approximately 2 weeks before forming a dry sclerotia, when they cease being conductive and is the prevalent limiting factor of their practical use; this is caused by dehydration and lack of nutrition, a limitation which may be overcome. The potential for Physarum wires in hybrid circuits is strengthened; while previous circuits were simple DC circuits, this work demonstrates that they may be used as electronic components or wires in both digital and analogue circuits or even as a computing component in analogue computers.

Physarum polycephalum: towards a biological controller.

Microbial fuels cells (MFCs) are bio-electrochemical transducers that generate energy from the metabolism of electro-active microorganisms. The organism Physarum polycephalum is a slime mould, which has demonstrated many novel and interesting properties in the field of unconventional computation, such as route mapping between nutrient sources, maze solving and nutrient balancing. It is a motile, photosensitive and oxygen-consuming organism, and is known to be symbiotic with some, and antagonistic with other microbial species. In the context of artificial life, the slime mould would provide a biological mechanism (along with the microbial community) for controlling the performance and behaviour of artificial systems (MFCs, robots). In the experiments it was found that P. polycephalum did not generate significant amounts of power when inoculated in the anode. However, when P. polycephalum was introduced in the cathode of MFCs, a statistically significant difference in power output was observed.

Polymalic acid-based nano biopolymers for targeting of multiple tumor markers: an opportunity for personalized medicine?

Tumors with similar grade and morphology often respond differently to the same treatment because of variations in molecular profiling. To account for this diversity, personalized medicine is developed for silencing malignancy associated genes. Nano drugs fit these needs by targeting tumor and delivering antisense oligonucleotides for silencing of genes. As drugs for the treatment are often administered repeatedly, absence of toxicity and negligible immune response are desirable. In the example presented here, a nano medicine is synthesized from the biodegradable, non-toxic and non-immunogenic platform polymalic acid by controlled chemical ligation of antisense oligonucleotides and tumor targeting molecules. The synthesis and treatment is exemplified for human Her2-positive breast cancer using an experimental mouse model. The case can be translated towards synthesis and treatment of other tumors.

Replication forks reverse at high frequency upon replication stress in Physarum polycephalum.

The addition of hydroxyurea after the onset of S phase allows replication to start and permits the successive detecting of replication-dependent joint DNA molecules and chicken foot structures in the synchronous nuclei of Physarum polycephalum. We find evidence for a very high frequency of reversed replication forks upon replication stress. The formation of these reversed forks is dependent on the presence of joint DNA molecules, the impediment of the replication fork progression by hydroxyurea, and likely on the propensity of some replication origins to reinitiate replication to counteract the action of this compound. As hydroxyurea treatment enables us to successively detect the appearance of joint DNA molecules and then of reversed replication forks, we propose that chicken foot structures are formed both from the regression of hydroxyurea-frozen joint DNA molecules and from hydroxyurea-stalled replication forks. These experiments underscore the transient nature of replication fork regression, which becomes detectable due to the hydroxyurea-induced slowing down of replication fork progression.