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Differentially expressed transcripts encoding P. polycephalum homologs of proteins involved in progesterone-mediated oocyte maturation. The figure shows screenshots taken from the KEGG database 25-27. Proteins encoded by up-regulated genes are shown in green, down-regulated ones in red. With kind permission by the Kanehisa Laboratories.
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Activation of a phytochrome photoreceptor triggers a program of Physarum polycephalum plasmodial cell differentiation through which a mitotic multinucleate protoplasmic mass synchronously develops into haploid spores formed by meiosis and rearrangement of cellular components. We have performed a transcriptome-wide RNAseq study of cellular reprogram...
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... we omit transcripts with weaker differential expression we see that transcripts with more than 6-fold changes encoded protein homologs known to control proliferation and differentiation like SOS, Ras, Ral, PI3K, PTEN, Akt/PKB, PKA, Rho and Arf being involved in Phospholipase D signaling and/or in other core signaling pathways. Figure 4 shows pathways of oocyte maturation and oocyte meiosis as retrieved from the KEGG data- base [25][26][27] . Proteins are highlighted with a colour code according to the mode of the differential regulation of the homolog-encoding mRNAs in P. polycephalum. ...
Citations
... Other 195 GenBank sequences corresponded to vouchered specimens of morphospecies absent in our sampling, or represented by a single individual, for which two DNA regions were publicly available. Finally, sequences corresponding to the four genes analysed here were bioinformatically extracted from the transcriptomes of Physarum polycephalum (Glöckner & Marwan 2017, accessible through http://www. physarum-blast.ovgu.de) ...
The class Myxomycetes consists of free-living protists characterised by their complex life cycle, which includes both microscopic (amoebae, flagellates and cists) and macroscopic stages (spore-bearing fruiting bodies, sclerotia, and plasmodia). Within it, the order Physarales , with more than 450 recognised species, constitutes the largest group. Although previous studies have shown the polyphyly of some of the traditionally accepted genera, its internal phylogenetic relationships have remained uncertain so far, and together with the lack of data for some key species, it prevented any taxonomic and nomenclatural revisions. We have compiled a substantially expanded dataset in terms of both taxon sampling and molecular data, including most of the genera described to date and four unlinked DNA regions, for which we provide partial sequences: nSSU, EF-1α , α-Tub , and mtSSU, analysed through maximum likelihood and Bayesian methods. Our results confirm that the family Didymiaceae is paraphyletic to the rest of Physarales . Within Didymiaceae s.lat., the recent reinstatement of the genus Polyschismium for most species traditionally ascribed to Lepidoderma , except for the type (Ronikier et al. 2022), is further supported here, as well as the definite inclusion of the genus Mucilago in Didymium and Lepidoderma s.str. ( L. tigrinum ) in Diderma (Prikhodko et al. 2023). Additionally, the genus Diachea is redefined to include some species previously treated in Physaraceae ( Craterium spp. with true columella). Within the monophyletic family Physaraceae , most genera are recovered as polyphyletic, suggesting that they should be no longer accepted as currently defined. However, the lack of resolution of some relationships within Physaraceae prevents us from resuscitating or creating several new genera to mitigate polyphyly. Among the well-defined groups with clear molecular signatures, we propose two taxonomic and nomenclatural changes at generic level: 1) a new genus, Nannengaella , is proposed for a major clade containing Physarum globuliferum and other species with heavily calcified sporophores and, often, a true calcareous columella; 2) Lignydium is resurrected for the clade containing Fuligo muscorum . Additionally, Trichamphora is suggested as the correct name for the clade containing Physarum pezizoideum . The taxonomy and nomenclature of some provisional genera, currently synonymous with Fuligo and Physarum , are disentangled, and we provide a comprehensive and updated nomenclatural conspectus that can be used when better resolved phylogenies are obtained. In total, 22 new combinations are proposed in different genera. A provisional key to the genera of the order is also provided.
... Public genomic and transcriptomic data from P. polycephalum were obtained from www.physarum-blast.ovgu.de and former published data [21,66]. Protein sequences from H. sapiens, M. musculus, D. rerio, D. melanogaster, X. laevis, C. elegans, A. trichopoda, A. thaliana, Z. mays, P. patens, T. thermophila, D. discoideum and S. cerevisiae were obtained from UniProt [67] and/or NCBI [68]. ...
... The Arabidopsis orthologue of PolE3 has not been faithfully identified yet [71] as well as orthologues for P. patens, T. thermophila, Z. mays, so these species were not included in the phylogenetic analysis. A local BLASTn (blast 2.6.0) was performed to identify chaperone homologs in the public P. polycephalum transcriptomes [21,66]. Identified transcripts were then aligned on the Physarum reference genome [21] to identify the corresponding genes. ...
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.
... To begin to address these outstanding questions, we performed spatially resolved RNA-seq on slime mold plasmodia under different growth conditions and single-nucleus RNA-seq on a slime mold plasmodium under different growth conditions at two time points (see Supplementary file 1 for sample overview). Sequencing reads were mapped against the Physarum transcriptome reference (Glöckner and Marwan, 2017;Schaap et al., 2015) with the data enabling localization of gene expression profiles to different structures within the plasmodium and exploration of local transcriptome responses, which correlated with nuclei heterogeneity. Taken together, our data suggests that nuclei within Physarum are mobile and can integrate local signals to coordinate a transcriptional response to dynamic environmental conditions, which enables the syncytium to locally change behavior and morphology. ...
... Interestingly, there is nuclei cluster 3 that expresses a glutamate receptor (GRLE) and a tyrosine-protein phosphatase (PTP2) both known to be involved in aggregation during fruiting body (sorocarp) development in the cellular slime mold Dictyostelium (Taniura et al., 2006;Ramalingam et al., 1993; Figure 3F). However, we observed neither morphological signs of fruiting body formation nor an enrichment in previously identified sporulation-related genes (Glöckner and Marwan, 2017) in this cluster (Figure 3-figure supplement 1E). Instead, we find the GO term 'Glycogen synthetic pathway' to be enriched in cluster 3 ( Figure 3-figure supplement 1) -a term also enriched in the oat-associated plasmodium SM4 (Figure 2-figure supplement 3H) and here for the secondary plasmodium in the region in direct contact with oat flakes in our experiment (Figure 3-figure supplement 1A). ...
... All sequenced datasets were aligned to the latest version of Physarum's transcriptome (Glöckner and Marwan, 2017). All raw reads were aligned using STAR (Dobin et al., 2013). ...
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.
... The species is distributed worldwide . During the reproductive phase, which is triggered by the activation of a phytochrome photoreceptor (Glöckner and Marwan, 2017), this myxomycete produces haploid spores through meiosis and rearrangement of cellular components. These small airborne spores can be widely dispersed by wind, giving the myxomycete access to a wide range of habitats. ...
... In addition, several AMP-activated protein kinase (AMPK) orthologs have been found in the P. polycephalum genome (Schaap et al., 2015). They are expressed in starving, sporulation-competent plasmodia (Glöckner and Marwan, 2017). When activated by low ATP levels, as, for example, during glucose deprivation, AMPK activation stimulates mitochondrial biogenesis and enhances catabolic processes. ...
... What makes the organism even more unique is the presence of bacterial and plant-type photoreceptors (e.g., phytochromes) as well as metabolic pathways and a cell cycle control system typically found in more complex eukaryotes. As an example, investigations of the transcriptome during developmental switching (i.e., photoreceptor-triggered activation of the sporulation pathway) show extensive remodeling of intracellular signaling networks (Glöckner and Marwan, 2017). In conclusion, P. polycephalum displays many interesting, complex, and versatile features, especially in the area of cell signaling, which are the basis and prerequisite for its dynamic behavior. ...
This chapter focuses not only on the cell biology and network dynamics of the myxomycete Physarum polycephalum but also includes a discussion of the convergent evolution of basal cognition. To that end, we provide insight on how myxomycetes interact with their environment, how they process information in the absence of a nervous system, and what makes them interesting for further research in decision-making and cellular intelligence. We focus on the biology and physics of the organism as well as on experimentally determinable aspects, including amoeboid locomotion and fluid dynamic signal processing, as well as network dynamics. One objective of this chapter is to contribute to the understanding of the complex behavior of myxomycetes in a mechanistic approach.
... Genomic and transcriptomic sequences from Physarum polycephalum were obtained from www.physarum-blast. ovgu.de and from further published data (6,15). Protein sequences from Homo sapiens, Mus musculus, Danio rerio, Drosophila melanogaster, Xenopus laevis, Caenorhabditis elegans, Amborella trichopoda, Arabidopsis thaliana, Zea mays, Physcomitrella patens, Tetrahymena thermophila, Dictyostelium discoideum and Saccharomyces cerevisiae were obtained from NCBI. ...
... In order to identify core histones, we used the Physarum reference genome and transcriptomes (6,15). We identified 15 histone-coding genes (one gene for H1, 3 genes for H2A, 3 genes for H2B, 5 genes for H3 and 3 genes for H4; see Materials and Methods) and 12 distinct transcripts. ...
... Finally, PpHTO1, PpHTB2 and PpHTT5 genes produce much less transcripts since their abundance is ∼2 (PpHTO1 and PpHTT5) or ∼10 (PpHTB2) million times smaller than the 19S transcript abundance. In addition, PpHTA1, PpHTB3 and PpHTF3 (Physarum polycephalum HisTone 2A 1, HisTone 2B 3 and HisTone Four 3) genes, which do not appear to be transcribed in sporulation-competent or sporulating plasmodia (15,33), were not detectably expressed in plasmodia and were not found in the genome of the TU291 strain we used for your study (Supplementary Figure S1A). ...
Physarum polycephalum belongs to Mycetozoans, a phylogenetic clade apart from the animal, plant and fungus kingdoms. Histones are nuclear proteins involved in genome organization and regulation and are among the most evolutionary conserved proteins within eukaryotes. Therefore, this raises the question of their conservation in Physarum and the position of this organism within the eukaryotic phylogenic tree based on histone sequences. We carried out a comprehensive study of histones in Physarum polycephalum using genomic, transcriptomic and molecular data. Our results allowed to identify the different isoforms of the core histones H2A, H2B, H3 and H4 which exhibit strong conservation of amino acid residues previously identified as subject to post-translational modifications. Furthermore, we also identified the linker histone H1, the most divergent histone, and characterized a large number of its PTMs by mass spectrometry. We also performed an in-depth investigation of histone genes and transcript structures. Histone proteins are highly conserved in Physarum and their characterization will contribute to a better understanding of the polyphyletic Mycetozoan group. Our data reinforce that P. polycephalum is evolutionary closer to animals than plants and located at the crown of the eukaryotic tree. Our study provides new insights in the evolutionary history of Physarum and eukaryote lineages.
... Giant, multi-nucleate cells, so-called plasmodia provide a source of macroscopic amounts of homogeneous protoplasm with a naturally synchronous population of nuclei, which is continually mixed by vigorous shuttle-streaming Guttes, 1961, 1964;Rusch et al., 1966;Dove et al., 1986). The differentiation of a plasmodium into fruiting bodies involves extensive remodeling of signal transduction and transcription factor networks with alterations at the transcriptional, translational, and post-translational level (Glöckner and Marwan, 2017). ...
... Morphogenesis then starts at about 11 h after the stimulus by the formation of nodules that subsequently culminate to form the fruiting bodies. Panel B was taken from Glöckner and Marwan (2017). ...
Dynamics of cell fate decisions are commonly investigated by inferring temporal sequences of gene expression states by assembling snapshots of individual cells where each cell is measured once. Ordering cells according to minimal differences in expression patterns and assuming that differentiation occurs by a sequence of irreversible steps, yields unidirectional, eventually branching Markov chains with a single source node. In an alternative approach, we used multi-nucleate cells to follow gene expression taking true time series. Assembling state machines, each made from single-cell trajectories, gives a network of highly structured Markov chains of states with different source and sink nodes including cycles, revealing essential information on the dynamics of regulatory events. We argue that the obtained networks depict aspects of the Waddington landscape of cell differentiation and characterize them as reachability graphs that provide the basis for the reconstruction of the underlying gene regulatory network.
... Giant, multi-nucleate cells, so-called plasmodia provide a source of macroscopic amounts of homogeneous protoplasm with a naturally synchronous population of nuclei, which is continually mixed by vigorous shuttle-streaming (Dove et al. 1986;Guttes 1961, 1964;Rusch et al. 1966). The differentiation of a plasmodium into fruiting bodies involves extensive remodeling of signal transduction and transcription factor networks with alterations at the transcriptional, translational, and post-translational level (Glöckner and Marwan 2017). ...
Dynamics of cell fate decisions are commonly investigated by inferring temporal sequences of gene expression states by assembling snapshots of individual cells where each cell is measured once. Ordering cells according to minimal differences in expression patterns and assuming that differentiation occurs by a sequence of irreversible steps, yields unidirectional, eventually branching Markov chains with a single source node. In an alternative approach, we used multinucleate cells to follow gene expression taking true time series. Assembling state machines, each made from single-cell trajectories, gives a network of highly structured Markov chains of states with different source and sink nodes including cycles, revealing essential information on the dynamics of regulatory events. We argue that the obtained networks depict aspects of the Waddington landscape of cell differentiation and characterize them as reachability graphs that provide the basis for the reconstruction of the underlying gene regulatory network.
... This enzyme belongs to a highly conserved protein family with orthologs in yeast (Saccharomyces cerevisiae (SNF1)) (Hedbacker and Carlson 2008), in other fungi, in plants (SnRK1) (Margalha et al. 2016), and in Dictyostelium discoideum (Bokko et al. 2007), a member of the amoebozoa group of organisms to which Physarum also belongs. Several AMPK orthologs are encoded in the P. polycephalum genome (Schaap et al. 2016) and are expressed in starving, sporulation-competent plasmodia (Glöckner and Marwan 2017). AMPK plays a role in cellular energy homeostasis. ...
Glucose deprivation in the slime mold Physarum polycephalum leads to a specific morphotype, a highly motile mesoplasmodium. We investigated the ultrastructure of both mesoplasmodia and non-starved plasmodia and found significantly increased numbers of mitochondria in glucose-deprived mesoplasmodia. The volume of individual mitochondria was the same in both growth forms. We conjecture that the number of mitochondria correlates with the metabolic state of the cell: When glucose is absent, the slime mold is forced to switch to different metabolic pathways, which occur inside mitochondria. Furthermore, a catabolic cue (such as AMP-activated protein kinase (AMPK)) could stimulate mitochondrial biogenesis.
... A related study performed the same analysis obtaining RNA from a single macroplasmodium at the two developmental stages; the study was in good agreement with the previous study using batches of cells (Barrantes et al., 2012). More recently, RNA-seq has been used to identify up and downregulation of signaling and regulatory genes during sporulation (Barrantes et al., 2012;Glöckner and Marwan, 2017). The transcriptome studies with competent and committed plasmodia build upon earlier studies where various sporulation mutants were characterized by demonstrating time-resolved somatic complementation (Marwan, 2003a,b;Marwan et al., 2005;Sujatha et al., 2005). ...
In recent decades, employing molecular genetic research methods to study myxomycetes has become increasingly important. The use of molecular approaches to the study of myxomycetes has occurred rather late compared to their use in other groups of organisms. Nevertheless, molecular studies are revealing information that was never before possible to obtain, allowing a better understanding of these unique and understudied amoeboid protists. This chapter is organized into two parts. In Part A, the molecular methods that have been applied in investigations of myxomycetes will be described, followed by a discussion of the ways in which these techniques have been used to enhance our understanding of myxomycete biodiversity and ecology. In Part B, molecular approaches to understanding the basic biology of myxomycetes will be reviewed.
Life evolved organisms to adapt dynamically to their environment and autonomously exhibit behaviors. Although complex behaviors in organisms are typically associated with the capability of neurons to process information, the unicellular organism Physarum polycephalum disabuses us by solving complex tasks despite being just a single although gigantic cell shaped into a mesmerizing tubular network. In Physarum, smart behaviors arise as network tubes grow or shrink due to the mechanochemical coupling of contractile tubes, fluid flows, and transport across the network. Here, from a physicist's perspective, we introduce the biology and active chemomechanics of this living matter network. We review Physarum’s global response in migration and dynamic state to its environment before revisiting its network architecture and flow and transport patterns. Finally, we summarize recent studies on storing and processing information to mount well-informed behaviors.
Expected final online publication date for the Annual Review of Condensed Matter Physics, Volume 15 is March 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
