E B Ridgway. When the organism can choose to travel through two different paths to a destination, the emergent behavior allows it … Funderud S, Andreassen R, Haugli F. DNA replication in Physarum polycephalum: electron microscopic and autoradiographic analysis of replicating DNA from defined stages of the S-period. 4A ), which suggests that the stimuli that control sporulation in P. polycephalum also act on intracellular cAMP levels by regulating RegA activity. We see this gene family expansion also in P. polycephalum , hinting at a common prerequisite for acquiring a plasmodial life stage. ER Thus, P. polycephalum offers an attractive model and alternative to yeasts for studying the functional dynamics of a mammalian cell-type mitotic cycle. For an ab initio gene prediction, we used Augustus ( Stanke et al. . Dove The reading frames for nitric oxide synthases found in P. polycephalum do not occur in the D. discoideum genome. L Yes. W Many of these SHKPs contain small molecule or light-sensing domains, such as the GAF, PAS/PAC, or phytochrome domains, which are likely to detect stimuli and activate phosphotransfer, whereas others contain protein kinase or AAA-ATPase domains. W JM 2011 ), opening up additional experimental avenues. Query for outgroup sequences mainly retrieved SHKPs, which also contain a receiver domain, and Dictyostelium RegA. Fragmin, homologous to severin in D. discoideum and gelsolin in more complex organisms ( Yin et al. The enormous size of the cell, the easy method of in vitro cultivation, the unique life cycle and its highly visible internal cytoplasmic streaming have made it invaluable for investigations on cell cycle regulation, differentiation, cytoskeleton and locomotion. 1990 ), was first described by the Hatano group ( Hasegawa et al. Ivanova Proteins that harbored the Interpro IPR000980 SH2 domain were retrieved from an Interproscan of all transcribed coding sequences. Accepted 16 August 2017 Hatano We propose a study of the boundaryeffects on the patterns and waves of the rhythmic contractions inplasmodia of Physarum polycephalum, a tractable model organism of theamoeboid type. Stanke These high-throughput methods combined with Mendelian genetics mitigate current difficulties of reproducibly making transgenic lines. . cGMP plays a role in the induction of sporulation in P. polycephalum ( Golderer et al. Five members of three classes of putative photoreceptors are expressed by P. polycephalum : one cryptochrome and one photolyase, one LOV-domain photoreceptor, and two phytochromes ( fig. S In fungi, alveolates, and oomycetes, a pentafunctional polypeptide is formed (AROM). In addition, we found 24 novel transfer RNAs, the spliceosomal U2 and U6 RNAs, 30 box C/D snoRNAs, 9 novel lncRNAs, which clustered into three groups by sequence similarity, as well as 24 RNAs shorter than 200 nucleotides clustering into three groups and 28 singleton RNAs shorter than 200 nucleotides ( Supplementary Spreadsheet 1 , second sheet). Lim 2015 ), which might represent a later rearrangement within the Amoebozoa clade. S21, Supplementary Material online) ( Schallenberg-Rüdinger et al. Here, we present an overview of the whole genome of P. polycephalum , focusing on some of its peculiar features such as its surprisingly extended signaling system. W.M. PD 1970. The mechanism of tube formation can be described as tubes become thicker in a given direction when shuttle streaming of the protoplasm persists in that direction for a certain time. et al. 1998 ; Du et al. S Within P. polycephalum , cytoplasm is shuttled in a peristaltic wave driven by cross-sectional contractions of tubes. Tero Schallenberg-Rüdinger The model organism most closely related to P. polycephalum for which a genome sequence has previously been determined is Dictyostelium discoideum ( Eichinger et al. It takes on many shapes and sizes throughout its life, morphing from microscopic amoeba to a multinucleate syncytium that can be several feet across and then forming millimeter-scale delicate, mushroom-like fruiting bodies. In fact, P. polycephalum has 64 nucleotidyl cyclases against 5 in D. discoideum. . Consequently, this type of actin phosphorylation in P. polycephalum is possibly not unique as suggested above. . . PubMed CAS Article Google Scholar Hatano, K. … P. polycephalum has a family of 43 of those proteins, suggesting a common requirement for amplification of these cyclases in some Amoebozoa. For a free-living, motile, phagocytotic, unicellular organism like P. polycephalum , physiologically relevant stimuli may include environmental factors such as light, humidity, temperature, pH, osmolarity, mechanical stress, or chemical signals released by mates, prey, predators, competitors, or symbionts . Skotheim The occurrence of open and closed mitosis in amoebae and plasmodia, respectively, is another well-known aspect of its rich cell biology ( Aldrich and Daniel 1982 ; Sauer 1982 ; Dove et al. Physarum polycephalum, an acellular slime mold or myxomycete, is a protist with diverse cellular forms and broad geographic distribution. V Nurse The presence of tyrosine kinases in both subdivisions of Amoebozoa, in their sister group Opisthokonta, and in other eukaryote divisions indicates that tyrosine kinases were likely present in the LCA to all eukaryotes and were selectively lost from many phyla. . Another unique finding is that riboflavin biosynthetic enzymes are encoded as two tri-functional reading frames ( supplementary fig . 2 ). As this specific experiment was performed on mitochondrial preparations, we only expect the more abundant nuclear small RNAs to be observed. . The number of cyclic nucleotide phosphodiesterases in P. polycephalum is about equal to that in D. discoideum and A. castellanii ( supplementary fig . 2015 ). More recently, P. polycephalum plasmodia have been used for studies ranging from cell biology and biophysics to unconventional computing for path finding, the biosensory control of robots, or the generation of music ( Tsuda et al. Mahendran . FB Marwan This becomes most obvious for cellular signaling through the extensive use of two-component signaling systems in parallel with RTK signal transduction. All transcriptome sequence data and files containing the gene loci-transcript conversion, the transcript map, and the automatic annotation of the reference transcriptome can be downloaded from http://www.physarum-blast.ovgu.de/ . H Apweiler 4B ). C R P Amoebal strains derived from different natural plasmodial isolates, such as Wis-1 and Wis-2 (see Appendix A of Supplemental Methods, Results , and Discussion), allow forward genetic approaches by mapping genes identified in phenotypic screens. P. polycephalum and D. discoideum reside in the other subdivision Conosa ( Schilde and Schaap 2013 ). Hasegawa Research on P. polycephalum lost its prominent role when animal cell culture and genetic techniques became more advanced, thereby replacing the slime mold as a state-of-the-art model. As a true free-living species, P. polycephalum should have retained most, if not all, components of such signaling systems inherited from the LCA of Amoebozoa. Two observations are particularly intriguing: In contrast to other Amorphea, P. polycephalum has a highly derived mitochondrial genome, the transcripts of which are affected by abundant and diverse types of RNA editing, including alterations of transcript sequences by nucleotide insertions and base conversions ( Mahendran et al. Sporulation of a starving plasmodium is induced by visible light or heat shock. U Loomis . For D. discoideum homologs with confirmed substrate specificity, gene names and kinase designation (TK and TKL:tyrosine; S/TK serine/threonine) follow the protein tags. . The transcriptome data were used to train this program according to the manual, and to provide splice information for the algorithm. If you have a user account, you will need to reset your password the next time you login. Downstream of the DNA-photolyase and FAD-binding domain of cryA is a short C-terminal part of approximately 100 amino acids encoded in the genomic sequence that is missing in Phypoly-transcript_04513 (gene locus 3553 and 3554), which shares greatest sequence similarity with DNA-photolyases and is designated as plyA (for photolyase A-type photoreceptor) and is presumably a DNA-photolyase rather than a sensory blue light photoreceptor. A. castellanii has even more (67), but 66 of these cyclases belong to a massively amplified family of transmembrane proteins that contain a cyclase domain, flanked by two protein kinase domains. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. See fig. This approach enabled us to define eight complete dyneins, one N-terminal half, and two N-terminal fragments. et al. . et al. S17, Supplementary Material online). HP Upon phosphorylation, the activity of the actin-fragmin complex changed to an F-actin capping function and was, therefore, a putative regulator of fast changes in local viscoelasticities in the F-actin network, a prerequisite for cytoplasmic streaming. During sporulation, the protoplasmic mass develops into multiple fruiting bodies. et al. Cross The G-protein coupled receptors (GPCRs) are a large and diverse family of transmembrane proteins in Metazoa and other eukaryotes that detect a broad range of physical and chemical stimuli. R In 2000, Japanese researcher Toshiyuki Nakagaki performed a seminal experiment showing that the slime mold is able to find the shortest route through a maze. 1998 ; Matveeva et al. Fifteen of these 90 appear to be of P. polycephalum mitochondrial origin and a further 13 are certainly contaminants from the sequencing process, as they have identity values higher than 85% to some bacteria and mouse sequences. PubMed. There is no common ancestor as in the case of divergent evolution of conventional protein kinases. Salzberg function as important cofactors (or their precursors) of various enzymatic reactions. The multitude and variety of cNMP binding domains and nucleotidyl cyclases in P. polycephalum indicates that cyclic nucleotide signaling is likely to play a very dominant role in its physiology and development. P. polycephalum has in addition 21 cyclases with highly variable functional domain architectures ( supplementary fig . D) Protein kinases. G Multi-objective shortest path problem (MOSP) plays an important role in practical applications, which seeks for the efficient paths satisfying several conflicting objectives between two nodes of a network. There is no need to keep a distinct amino acid sequence with a certain arrangement of protein domains, just structure/function relationships count. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Alkylglycerol monooxygenase and nitric oxide synthase, in its full length form with oxygenase and reductase domains, are regularly found only in animals. In P. polycephalum, sporulation is induced by light and this induction was shown to be mediated by a phytochrome-type receptor ( Starostzik and Marwan 1995b ). 2012 ) and the presence of 21 tyrosine kinases in A. castellanii ( Clarke et al. Research Article An Improved Physarum polycephalum Algorithm for the Shortest Path Problem XiaogeZhang, 1 QingWang, 1 AndrewAdamatzky, 2 FelixT.S.Chan, 3 Sankaran Mahadevan, 4 andYongDeng 1,4 School of Computer and Information Science, Southwest University, Chongqing , China Unconventional Computing Center, University of the West of England, Bristol BS QY, UK Our analysis highlights a wealth of interesting molecular features and will help in enabling work at the molecular level in combining the well-established classic genetics with second-generation sequencing approaches. The SH2 domain is too small for meaningful sequence alignment-based phylogeny reconstructions and proteins are therefore classified by their protein domain architecture. S18, Supplementary Material online) that are involved in chromophore binding and crucial for the photochemical properties of phototropin-type photoreceptors ( Heintzen 2012 ). Small non-coding RNAs perform important functions in all organisms, but can be difficult to annotate de novo owing to their short length and their poorly defined sequence patterns. Virtually all aspects discussed here characterize P. polycephalum as an organism with higher molecular complexity than other sequenced Amoebozoa. Sequence alignment with the most similar phytochromes suggests that the chromophore-binding site may be a cysteine close to the N-terminus that is conserved between P. polycephalum PhyA and PhyB and various bacterial phytochromes, whereas the cysteine of the CHxxYxxNMG motif that serves as a chromophore-binding site in plant phytochromes is replaced by valine in the two P. polycephalum proteins ( supplementary fig . The plasma membrane-attached cortical system can be labeled with TRITC-G-actin as well … S A total of 34,438 gene loci were defined in this way ( table 1 ), half of which are represented by transcripts (17,158). Sauer Individual pieces cut off from a single plasmodium maintain synchrony, providing unique experimental options for single-cell biology. Using plasmodia ranging in size from 100 μm to 10 cm, we investigated the size dependency of their thickness distributions and locomotion speeds during free locomotion. Morgenstern The uninucleate cells that form part of the life-cycle (the ‘amoebae’), in two-membered culture with Pseudomonas fluorescens, were found to be suitable for handling by some of the standard techniques of microbial genetics, including plating. Fuller K T Kuehn . One species in particular, the SpongeBob SquarePants–yellow Physarum polycephalum, can solve mazes, mimic the layout of man-made transportation … Export citation and abstract M By analyzing macroscopic samples taken at regular time intervals from a single plasmodial cell at subsequent points of a time series, one can exploit the remarkable natural mitotic synchrony of plasmodial nuclei (see Supplementary Results and Discussion) and resolve time-dependent regulatory events within individual cells at transcriptome and proteome-wide scales. Zdobnov Kinesins have a wider length range than the other motor proteins, and the regions outside the motor domain are highly variable. Becker Construction of gene models therefore heavily relied on accompanying transcriptome data (see Materials and Methods). . Grigoriev At least two photoreceptors, a phytochrome-like and a blue light photoreceptor, act synergistically in controlling sporulation in P. polycephalum in response to far-red and to blue light ( Starostzik and Marwan 1995a , 1995b ; Lamparter and Marwan 2001 ) (for details see Supplementary Methods, Results , and Discussion), but these receptors had not been identified at the molecular level. . S21A, Supplementary Material online). Harashima We removed from the assembly all contaminating sequences, trimmed vectors (X), and ambiguous bases (N). The unresolvable sequence patches cause innumerable gaps in the final sequence, resulting in a mean scaffold size of only slightly larger than 2 kb. Combined sequence reads from different libraries (including 3- and 8-kb mate pairs) were assembled using the Newbler software version 2.6 ( Margulies et al. 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