M . A) G-protein coupled receptors. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. 1986 ). Schleicher TG LN Originally considered to be plant-specific photoreceptors, phytochromes regulate many aspects of metabolism, motility, gene regulation, and development ( Heintzen 2012 ). View Physarum Polycephalum Research Papers on Academia.edu for free. For the 24 genes analyzed in supplementary table S5 encoding for 26 enzymes, closest orthologs for 12 were found in Amoebozoa (eight of these in Dictyosteliida ), six in bacteria, four in animals, three in Capsaspora owczarzaki , an Opisthokonta of uncertain placing, and one in red algae ( supplementary table S5 ). We next trained the gene prediction program Augustus ( Stanke et al. P Abundance of nucleotidyl cyclases, cAMP or GMP binding proteins, and cyclic nucleotide phosphodiesterases. This set is dominated by proteins with two sets of six transmembrane domains that flank two cyclase domains. As Opisthokonta and Amoebozoa form together the Amorphea ( Adl et al. G 2011 ), opening up additional experimental avenues. G Cunningham Citation Christina Oettmeier et al 2017 J. Phys. Physarales is of particular interest since the two best-studied myxomycete species, Physarum polycephalum and Didymium iridis, belong to this order and are currently subjected to whole genome and transcriptome analyses. Kamiya Margulies Werner-Felmayer The cyclic nucleotides cAMP, and to a lesser extent cGMP, are widely used as intracellular second messengers for a broad range of external stimuli in all domains of life. W Search for other works by this author on: Evolutionary origin of cAMP-based chemoattraction in the social amoebae, A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins, Involvement of the second messenger cAMP in gravity-signal transduction in, 9th Conference on Interdisciplinary Musicology – CIM14. 2011 ). Schmitz-Linneweber Here we report molecular phylogeny based on ribosomal DNA … The PAS_9 domain of the predicted P. polycephalum LovA protein contains the highly conserved NCRFLQ motif with the cysteine residue serving as a potential chromophore-binding site embedded in additional highly conserved residues ( supplementary fig . Nezvetskii Schedl S14, Supplementary Material online), as compared with 12 in D. discoideum and 6 in A. castellanii. Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. Solnica-Krezel Physarum polycephalum est une espèce de myxomycètes de la famille des Physaraceae, vivant dans des zones fraîches et humides telles que les tapis de feuilles des forêts ou le bois mort. Another unique finding is that riboflavin biosynthetic enzymes are encoded as two tri-functional reading frames ( supplementary fig . The light-sensing part of this photoreceptor is likely to be the phytochrome domain that is present in two P. polycephalum SHKPs (see below; fig. As mating of amoebal cells and plasmodium formation are controlled by different mating type genes, sophisticated approaches based on Mendelian genetics are possible ( Dee 1987 ). et al. GD • Future applications can exploit the power increase from a MFC as a bio-controller. Domain architecture of the predicted photoreceptors encoded in the P. polycephalum transcriptome as determined by searching the NCBI Conserved Domain Database ( Marchler-Bauer et al. 1A ) is very useful for the generation and analysis of mutants ( Dee 1982 , 1987 ). Cross 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. Liu RIS. C . Top and bottom gray rows are common cell-cycle gene names from Homo sapiens and Arabidopsis thaliana , respectively. The model organism most closely related to P. polycephalum for which a genome sequence has previously been determined is Dictyostelium discoideum ( Eichinger et al. In contrast, there are only a few documented roles for cAMP or cGMP in P. polycephalum. For detailed information on strains used, preparation of nucleic acids, and for bioinformatic methods, see supplementary file 1 . 2001 ; Bundschuh et al. Further analysis of domains revealed that 304 domains were present at least once in the genomes of P. polycephalum and A. castellanii , but absent from D. discoideum ( supplementary table S2 ). Gunji J M 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. W Polsakiewicz This suggests that the majority of unsupported gene loci may represent false-positive predictions, which is fairly typical of highly fragmented genome assemblies. E To evaluate the prevalence of cAMP and cGMP signaling in P. polycephalum , we investigated the presence of the cyclases, binding proteins, and phosphodiesterases that, respectively, synthesize, detect, or degrade cyclic nucleotides. Wiley Interdiscip Rev Membr Transp Signal. S21, Supplementary Material online) ( Schallenberg-Rüdinger et al. Messner RegA and one other none-SHKP outgroup sequence (YP_005167077) were aligned with the P. polycephalum sequences, and a phylogenetic tree was constructed by Bayesian inference as described above. Apogamic development can be suppressed experimentally by elevated temperature, which allows propagation of amoebal clones or the formation of a diploid plasmodium by mating of two amoebae of different mating type. 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. . 2011 ). et al. How an individual communicates across its network remains a puzzle, but Physarum polycephalum has emerged as a novel model used to explore emergent dynamics. H JM A . G et al. C A total of 29 proteins contained the IPR020635, IPR008266 identifiers for Y protein kinases, but only four of those showed full consensus with validated tyrosine kinase-specific sequences (see fig. Suga Tsuda H 2013 ). . Sub-families or alternative names of cell-cycle genes are listed in parentheses. SK Find out more about journal subscriptions at your site. HW Since the time of its first description, it has been the subject of a multitude of cell biological, biochemical, genetic, and lately physical studies. Two phytochrome genes, phyA and phyB , are expressed in P. polycephalum , partially encoded by transcripts 20261 (gene locus 28349) and 03416 (gene locus 5996), respectively. 1992 ; Eichinger et al. 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. P K We show that in asynchronous sequential logic gates we can erase … 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. 1998 ; Du et al. Entamoeba histolytica genes were omitted for calculating the tree, because endoparasites are known to evolve at different rates as compared with free-living organisms. Physarum polycephalum is a free-living amoebozoan protist displaying a complex life cycle, including alternation between single- and multinucleate stages through sporulation, a simple form of cell differentiation. physarum polycephalum videos and latest news articles; GlobalNews.ca your source for the latest news on physarum polycephalum . Gruter These domains could be downstream effectors, which are regulated by phosphorelay. The DYW-type PPR protein families of Physarum polycephalum, Naegleria gruberi, and the moss Physcomitrella patens, for example, cluster taxon-wise without evidence for recent HGT ( supplementary fig . S20, Supplementary Material online). Accepted 16 August 2017 The response regulator subsequently regulates the activity of an effector, such as an enzyme or transcription factor. A 1999 ). Isolation from vegetative cells of. Cell. In the current study, many major families of actin-binding proteins have been found ( Supplementary Spreadsheet 2 ). Loomis Several such DYW-type PPR proteins have been characterized as site-specific C-to-U editing factors in plants. 4 for phylogenies and functional domain architectures of the proteins. S When the organism can choose to travel through two different paths to a destination, the emergent behavior allows it … King Published 15 September 2017, Method: Single-blind . J Cytol.63: 1–58. Kuo Matching possible kinesin gene loci with transcript data yielded 39 defined loci. Spottswood Kuehn Furthermore, another surprising feature is the comparatively frequent presence of homologous enzymes that catalyze the same enzymatic reaction, whereas most species including D. discoideum use only one. The identifiers of P. polycephalum proteins with full tyrosine kinase consensus are underlined. This suggests an ancient origin of this typically animal-type signaling enzyme and its signal transduction mechanism via cGMP. This initial analysis yielded 733,443 potential transcripts. P To gain access to this content, please complete the Recommendation ( B ) Receivers. The established lab strains of D. discoideum do not form viable progeny after mating, which hinders genetic experiments, whereas mating of strains and segregation of meiotic progeny in P. polycephalum is under ready experimental control. Doonan M Even peculiar actin isoforms like D. discoideum filactin, an actin with a large N-terminal extension ( Joseph et al. For details, see Supplemental Methods, Results , and Discussion. JH See Supplemental Methods, Results , and Discussion for predicted chromophore-binding sites. 1991 ), the availability of its genome sequence now provides unique opportunities to study the functional dynamics of the regulation of mitosis, meiosis, and the coregulation of cell cycle and cell fate decision. The plasmodium keeps growing as long as environmental conditions are favorable. Richards V Fluorescently labeled actin (TRITC-G-actin) and heavy meromyosin (TRITC-HMM) derived from skeletal muscle and injected into microplasmodia of the acellular slime mold Physarum polycephalum were used to analyze the function of a cortical and fibrillar actin system in living specimens. The profilins as members of G-actin sequestering proteins, fragmin as representative of the Ca 2+ -dependent F-actin severing proteins, the heterodimeric F-actin capping proteins (formerly “ Physarum beta-actinin”), F-actin crosslinking proteins like alpha-actinin and filamin, myosins as major motor proteins, and formin-like proteins with FH1 and FH2 domains are present in comparable numbers as in D. discoideum and more complex organisms. Wohlfarth-Bottermann This is 1.5- and 1.2-fold more than in D. discoideum and A. castellanii , respectively, and, therefore, a more modest increase than observed for the other signal transduction proteins described above. The Physarum machine is a biological computing device, which employs plasmodium of Physarum polycephalum as an unconventional computing substrate. J P. polycephalum and D. discoideum reside in the other subdivision Conosa ( Schilde and Schaap 2013 ). In eukaryotes including mammalian cells, much of the sensory input directly or indirectly feeds into the control of the mitotic or meiotic cell cycle as part of the sensory control of developmental decisions or programs. Phypoly-transcript_04617 ( cryA, cryptochrome-like photoreceptor ; gene locus 1148 ) encodes a protein with highest similarity to chicken cryptochrome-2 and other related animal cryptochromes. 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. DL Buchler ( A ) Sensor histidine kinases/phosphatase. P. polycephalum has 18 SH2 domain proteins ( fig. The reading frames for nitric oxide synthases found in P. polycephalum do not occur in the D. discoideum genome. . . The mean length of the others is well above 700 amino acids. The sequences of the most consensual P. polycephalum tyrosine kinases were aligned with those of their closest homologs in other species. Sequences were first aligned with all their closest relatives in other organisms, as identified by BlastP of the GenBank non-redundant sequences. Inspection of the P. polycephalum transcriptome revealed the presence of a total of 447 proteins with S/T, Y, or S/T/Y (dual specificity) kinase domains (see Supplemental Methods, Results , and Discussion and table 3 for further details). Schnittger Dove 3 ). Christina Oettmeier3,1, Klaudia Brix2 and Hans-Günther Döbereiner3,1, Published 15 September 2017 • Heidel 1993 ). L . 1986 ; Burland et al. R M 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. Physarum polycephalum, literally the 'many-headed' slime mold, is a giant multi–nucleated but unicellular protist. In conclusion, among the unicellular genetic model organisms, P. polycephalum displays many features of animal cells and, with respect to its molecular complexity, the cross-talk of signaling molecules, and the resulting dynamic behavior. . After clustering with usearch ( Edgar 2010 ), we obtained 31,770 clusters, each represented by the largest sequence in a cluster. . By continuing to use this site you agree to our use of cookies. . The protein kinases that modify the function of downstream effector proteins by phosphorylation of serine/threonine (S/T) or tyrosine (Y) residues are the most common intermediates of signal processing cascades. Physarales represents the largest taxonomic order among the plasmodial slime molds (myxomycetes). S21C, Supplementary Material online). 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. FB Methylation of the deoxyribonucleic acid of Physarum polycephalum at various periods during the mitotic cycle. NB Recent reviews have suggested that the metazoan regulatory proteins E2F, Rb, and Cyclin D may constitute the primitive G1/S control system found in most eukaryotes ( Doonan and Kitsios 2009 ; Cross et al. H Each entry is a conservative estimate of the number of family members in each genome. 1990 ) that is missing in P. polycephalum. M DYW-type PPR proteins in a heterolobosean protist: plant RNA editing factors involved in an ancient horizontal gene transfer? 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. Amoebae have four developmental options. Domains enriched compared with those of A. castellanii and D. discoideum include transposon domains and, again, domains associated with signaling functions ( supplementary table S3 ). • P. polycephalum alone does not generate an electrical current in a MFC anode electrode. Joseph Clarke S See supplementary figs S15 and Supplementary Data for phylogenies and functional domain architectures of cyclases and phosphodiesterases. . S 2015 ), which might represent a later rearrangement within the Amoebozoa clade. Hunter Rabien Within P. polycephalum , cytoplasm is shuttled in a peristaltic wave driven by cross-sectional contractions of tubes. 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