physarum polycephalum article

PPR proteins are sequence-specific RNA-binding proteins that act in diverse processes of RNA maturation, mainly in mitochondria and chloroplasts ( Schmitz-Linneweber and Small 2008 ). Humans have 518 protein kinases and even yeast has over a hundred ( Hanks 2003 ). Thiery . Rüdinger The last common ancestor of Amoebozoa and Opisthokonta is known as Amorphea ( Adl et al. Physarum, or more precisely Physarum polycephalum, is an acellular slime mold, or myxogastrid. Daniel In terms of distinct domains, A. castellanii and P. polycephalum are similar, whereas fewer types of domains have been identified in D. discoideum, suggesting domain loss in the social amoebae ( table 2 ). Volume 50, The version described in this paper is the first version, GDRG01000000. Beilina M The slime mould Physarum polycephalum was incorporated into a series of MFCs. The methods used for sequence alignment, alignment editing, and Bayesian phylogenetic inference are the same as described in the legend to supplementary fig S13 . E B Ridgway. 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. Araki Grigoriev . S Abundance of nucleotidyl cyclases, cAMP or GMP binding proteins, and cyclic nucleotide phosphodiesterases. 2012 ). Cell cycle variation in cyclic adenosine 3',5'-monophosphate-dependent inhibition of protein kinase from, Spectroscopic detection of a phytochrome-like photoreceptor in the Myxomycete, Phosphotyrosine signaling: evolving a new cellular communication system, Evolution of SH2 domains and phosphotyrosine signalling networks, RNA editing by cytidine insertion in mitochondria of, Genome sequencing in microfabricated high-density picolitre reactors, Involvement of cyclic adenosine monophosphate in the control of motile behavior of, Universal control mechanism regulating onset of M-phase, Nobel lecture: cyclin dependent kinases and cell cycle control, Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements, Plant-type mitochondrial RNA editing in the protist, Synchronization of mitosis by the fusion of the plasmodia of. Christina Oettmeier3,1, Klaudia Brix2 and Hans-Günther Döbereiner3,1, Published 15 September 2017 • Braund Much of our knowledge of the molecular mechanisms controlling progression through the eukaryotic cell cycle has come from studies of model organisms, notably Fungi (budding yeast and fission yeast) and Metazoa (frog and fruit fly embryos and mammalian cell lines). S21A, Supplementary Material online). It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. There is also a homolog of D. discoideum PdeE, in which an intrinsic Lactamase_B domain acts as a cAMP phosphodiesterase. 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. EM Burland WF We ran tRNAscan-SE (PMID: 9023104) with default parameters on the genome, which resulted in 319 putative tRNA loci and 248 unique putative tRNA sequences ( Supplementary Spreadsheet 1 , third sheet). JW Given that in its natural environment there is direct physical contact with the slime mold growing on decaying plant materials, horizontal gene transfer (HGT) from plants may be a possible source of the P. polycephalum PPR genes. P In addition, there are putative cNMP binding proteins with additional RhoGEF, VWA, and P2X receptor domains that are not present in other organisms. 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 In the course of its complex life cycle ( fig. Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. RIS. . SM L Entamoeba histolytica genes were omitted for calculating the tree, because endoparasites are known to evolve at different rates as compared with free-living organisms. We found at least 146 GPCRs, with representatives from all families except family 4, the fungal pheromone receptors ( supplementary fig . In recent years, research on P. polycephalum has again become cutting-edge. et al. During sporulation, the protoplasmic mass develops into multiple fruiting bodies. Journal of Physics D: Applied Physics, Thus, the evolutionary pressure is on the structure of the molecule in determining its function. A BLAST search of the PAS_2, GAF, PHY domain portion of the proteins against the UniProt database revealed closest similarity to Nostoc PHYA (Q9LCC2) and four other bacterial phytochromes, followed by plant phytochromes. Building on early, pioneering studies of eukaryotic cell-cycle regulation in P. polycephalum ( Rusch et al. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. Ivanova The P. polycephalum genome contains ∼51 SHKPs with a large variety of different functional domain architectures ( fig. This initial analysis yielded 733,443 potential transcripts. There are scores of complex repeats in the genome, which contains a minimum of 484 integrase domains (PF00665) and 1,014 reverse transcriptase domains (PF07727 and PF00078). Nucleic Acids Res. 5 ). In Metazoa, tyrosine phosporylated substrates become binding sites for SH2 domain proteins, which further transduce the response ( Liu and Nash 2012 ). J GD Physarum polycephalum is a myxomycete, or plasmodial slime mold. A second phylogeny was constructed from these outgroup and P. polycephalum sequences, using only segments encompassing the HisKA, HATPase-c, and receiver domains, which are common to all or most retrieved SHKPs. SK . et al. Pteridine work was funded by the Austrian Science Fund (FWF), P22406 to E.R.W. P. polycephalum and D. discoideum reside in the other subdivision Conosa ( Schilde and Schaap 2013 ). LN D. discoideum is a cellular slime mold where differentiation occurs in developmentally interacting cells, whereas in the acellular slime mold P. polycephalum, a single, multinucleate plasmodial cell differentiates in a manner reminiscent of Drosophila embryos or other developing syncytia. . The key decision point for proliferation and development in animal cells occurs in G1 phase. Hayashi It was shown previously that a plasmodial species, Reticulomyxa filosa , has amplified its complement of kinesin domain-bearing genes, which may be associated with the increased requirements of intracellular transport in a huge cell ( Glöckner et al. Takahashi 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. S20, Supplementary Material online). Google Scholar. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. et al. PubMed. Search for other works by this author on: This Site. It contains enzymes for the biosynthesis of 7-aminomethyl-7-deaza guanine (preQ1), a precursor for the special tRNA base queuosine (Q), as well as for the biosynthesis of riboflavin. Cet amibozoaire a été classé depuis 2015 dans les mycétozoaires1. Since the time of its first description, it has been the subject of a multitude of cell biological, biochemical, genetic, and lately physical studies. E The domain composition of the predicted protein and the highly conserved residues for chromophore binding in the PAS_9 domain suggests that LovA may act as an unconventional blue light photoreceptor that integrates, modulates, and/or relays multiple signals and might even bind DNA through its PAS_9 domain. 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. Ten further fragments of varying length show homology to the middle and C-terminal parts of dyneins. J . 4B ). HP Clarke P. polycephalum also has a close homolog of D. discoideum SGC, a guanylate cyclase that is involved in chemotaxis, and it has a close homolog of D. discoideum and A. castellanii AcrA, an adenylate cyclase that is essential for spore maturation in D. discoideum ( Loomis 2014 ). The retrieved sets largely overlapped, but the transcriptome (Phypo identifiers in the tree) contained both the largest number and more complete SHKPs. H 2015 ), which might represent a later rearrangement within the Amoebozoa clade. Messner Schaap K . In addition, the transcriptome sequences provide the basis for quantitative proteomic approaches by mass spectrometry. . We then fused predicted genes and reference transcripts to gene loci if predicted genes were covered by the same reference transcript and/or if predicted genes were present in the near vicinity (<50 bases apart) and at least one of them was covered or partially covered by a transcript sequence. et al. 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. A) G-protein coupled receptors. Harashima Based on sequence similarity, GPCRs are subdivided into six families, where members of each family detect different sets of ligands. It is unusual in switching between open … There are distinct classes of chromoproteins that act as photoreceptors in both prokaryotes and eukaryotes in sensing the visible part of the spectrum including near UV: cryptochromes, LOV-domain photoreceptors, rhodopsins, and phytochromes ( Heintzen 2012 ). 1970 Dec 10; 245 (23):6436–6441. In fact, P. polycephalum has 64 nucleotidyl cyclases against 5 in D. discoideum. 4 for phylogenies and functional domain architectures of the proteins. The reasons for or advantages of this apparent redundancy are currently unknown. R Dove A The P. polycephalum genome also contains genes encoding enzymes for complete shikimate and aromatic amino acid synthesis pathways, which are not present in either the social amoebae or Entamoebae ( Richards et al. Carroll Sequences were first aligned with all their closest relatives in other organisms, as identified by BlastP of the GenBank non-redundant sequences. 2014 ), have probably taken over their role in these phyla. Find out more about journal subscriptions at your site. There is no common ancestor as in the case of divergent evolution of conventional protein kinases. See fig. Proteins with S/T, S/T/Y, or Y protein kinase domains were retrieved from an Interproscan of all transcribed coding regions by the presence of the Interpro IPR002290, IPR008271, IPR001245, IPR020635, and/or IPR008266 domains. King Dee How an individual communicates across its network remains a puzzle, but Physarum polycephalum has emerged as a novel model used to explore emergent dynamics. These included tRNAs for all 20 amino acids as well as 6 putative tRNA-SeC loci (each with a unique sequence) and four putative tRNA loci of undetermined type (each with a unique sequence). . This greatly exceeds the number present in other Amoebozoa species such as A. castellanii and D. dis c oideum , which contain only 38 and 118 reverse transcriptase domains, respectively. Buchler Domains enriched compared with those of A. castellanii and D. discoideum include transposon domains and, again, domains associated with signaling functions ( supplementary table S3 ). The plasmodium keeps growing as long as environmental conditions are favorable. Physarum polycephalum: a review of a model system using a structure-function approach. Among these are a considerable number of domains associated with signaling functions. . [PMC free article] Bird A. AR Please choose one of the options below. S 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. Thus, the mean number of confirmed introns per gene is approximately 5. In total, P. polycephalum complex repetitive elements contribute approximately 3 Mb or 1.3% to the size of the genome ( supplementary table S4 ). Kamiya M T De Ville Kinesins have a wider length range than the other motor proteins, and the regions outside the motor domain are highly variable. WF 1966 ; Sachsenmaier et al. Plattner-Schobel J Physarum polycephalum. Skotheim Whereas most P. polycephalum response regulators have no additional features, two have leucine-rich repeats and two have a phosphodiesterase domain and are closely related to the D. discoideum cAMP phosphodiesterase RegA ( fig. A C Durham, A C Durham Search for other works by this author on: This Site. Physarum polycephalum belongs to the Amoebozoa, the sister group to the Opisthokonts (i.e., fungi and animals) ( Cavalier-Smith 2003 ) which both together form the supergroup Amorphea ( Adl et al. 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. et al. If those mechanisms can be found in as primordial an organism as a slime mold, it could fundamentally change our perception of the nature and evolution of cognition. L . . ( A ) Section of the alignment that is essential for peptide substrate recognition, with residues essential for all protein kinases in blue text, for tyrosine kinases in red text, and for S/T or S/T/Y kinases in green. JH The plasma membrane-attached cortical system can be labeled with TRITC-G-actin as well … Form and we will follow up with your librarian or Institution on your behalf. NE 2008 ). function as important cofactors (or their precursors) of various enzymatic reactions. The article, written by Rex Merrifield, is currently the number one most popular article on the Horizon website (2pm 25th February 2015 UK time) You can … Read more › Posted in News Tagged with: PhyChip , physarum polycephalum , slime mould I The genetic material used for sequencing the P. polycephalum genome was derived from axenic, haploid amoebal cells (strain LU352). N Photoreceptor domains that are light-sensitive through covalently or non-covalently bound chromophores are often attached to signaling domains that relay the photosensory output to the cellular signaling network. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 4 . Fuller S15, Supplementary Material online). Waack They can propagate by cell division through an open mitosis or differentiate into a flagellate, a cyst or a multinucleate plasmodium. Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. . Apweiler et al. This way we predicted 47,779 protein coding genes. cGMP plays a role in the induction of sporulation in P. polycephalum ( Golderer et al. 2004 ). H Nash With some 100 PPR protein genes, P. polycephalum features much more than tenfold the number found in other slime mold genomes such as Polysphondylium pallidum or D. discoideum. Predicted genes without transcript coverage and no transcript in the near vicinity (<50 bp apart) were counted as independent gene loci. The median size of the 160,988 introns confirmed by transcript data is 231 bases, and the total number of predicted introns is 676,387. . R DL C If only the genes with transcript data are counted, the number of introns per gene increases to well above 9. H P. polycephalum possesses a wealth of motor domains. The tree was decorated with protein domain architectures. Cell. Purchase this article from our trusted document delivery partners. 1993 ). Physarum polycephalum is a large, single-celled amoeboid organism forming a dynamic tubular network connecting the discovered food sources during foraging. The basic mechanisms with which organisms perceive their environment, integrate this information and make decisions based on this input are investigated. Google Scholar . management contact at your company. G RNAs transcribed from the mitochondrial genome of Physarum polycephalum are heavily edited. . ( A ) Schematic representation of the different stages that form during the heterothallic or the apogamic life cycle, as represented by the outer or the inner circle, respectively. However, because in the current assembly some shorter introns and exons are missing in scaffolds owing to simple repeat sequences at both ends, we used the reference transcripts together with the gene predictions to define gene loci. 2011 ), opening up additional experimental avenues. In fact, the set of PPR proteins present in P. polycephalum is significantly larger than in other Amoebozoa and, more broadly, within the Amorphea super-domain at large. and The Genome Institute at Washington University School of Medicine. As in other taxa, the P. polycephalum proteins contain PPR arrays of variable sizes ranging from only a few up to more than 20 tandem PPRs in individual proteins. The most prevalent editing event is the insertion of single Cs, with Us and dinucleotides also added at specific sites. Lim W Isolation from vegetative cells of. P. polycephalum is much more diverse than D. discoideum in its pteridine metabolic equipment. Fragmin, homologous to severin in D. discoideum and gelsolin in more complex organisms ( Yin et al. Physarum polycephalum, a fast-growing species, is the most notable; it has been used widely in physiological experiments in protoplasmic streaming and nuclear behaviour. 1970. Mahendran 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 . Burland Schaap The aim is to find underlying universal mechanisms of decision making and awareness. Hanks Earl Ettienne From the Department of Biological Sciences, State University of New York at Albany, Albany, New York 12203. . In the current study, many major families of actin-binding proteins have been found ( Supplementary Spreadsheet 2 ). papers2://publication/uuid/AC77D621‐D506‐4D95‐A026‐AC65533A364F; 2014 Mar 12: Berlin, Complete characterization of the edited transcriptome of the mitochondrion of, Patterns of inheritance, development and the mitotic cycle in the protist, Protist phylogeny and the high-level classification of Protozoa, Evolution of networks and sequences in eukaryotic cell cycle control. TG In fungi, alveolates, and oomycetes, a pentafunctional polypeptide is formed (AROM). Thus, only a minor fraction of transcripts is not represented by the assembled genome. A cAMP is particularly important for Dictyostelid development, where it regulates encystation, progression through multicellular development, maturation of spore and stalk cells, and maintenance of spore and cyst dormancy by acting on PKA ( Schaap 2011 ). SK Upon sporulation, the low number of diploid nuclei that have been formed within the plasmodium gives rise to viable spores. P We searched all defined gene loci for the presence of such domains. 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 ). Nezvetskii Originally considered to be plant-specific photoreceptors, phytochromes regulate many aspects of metabolism, motility, gene regulation, and development ( Heintzen 2012 ). The Physarum machine is a biological computing device, which employs plasmodium of Physarum polycephalum as an unconventional computing substrate. P. polycephalum has for long been a classic model organism in cell biology. . 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. Physarum cinereum, which forms an ashy-gray coating on lawn grasses under special conditions of moisture and humidity, is unsightly but harmless and…. The computer you are using is not registered by an institution with a subscription to this article. . 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. 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. RC Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer. Kuo This becomes most obvious for cellular signaling through the extensive use of two-component signaling systems in parallel with RTK signal transduction. Schleicher The tree is based on 30 highly conserved genes and rooted with other eukaryotes. 2015 ). This resulted in the confirmation of many known small P. polycephalum RNAs ( Supplementary Spreadsheet 1 , first sheet). The P. polycephalum genome was queried by BLAST with all 15 Dictyostelid SHKPs, plant and fungal SHKPs, and the most divergent prokaryote SHKPs, while transcribed proteins were queried for the presence of Interpro domains IPR003661 and IPR003594 for the HisKA and HATPase-c moieties of SHKPs, respectively. The essentials of DNA methylation. These data lead to major conclusions: The actin-fragmin kinase is clearly an example for convergent evolution. The methods described in the legend to supplementary fig S13 were used for phylogenetic inference. Even peculiar actin isoforms like D. discoideum filactin, an actin with a large N-terminal extension ( Joseph et al. P. polycephalum has 18 SH2 domain proteins ( fig. . . R 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. 2013 ), a member of Lobosa, one of the two major subdivisions of Amoebozoa. 2005 ), and the Newbler contigs were then assembled into scaffolds using Bambus version 2.3 ( Pop et al. Morgenstern K As in plants and Naegleria , the residues likely coordinating a zinc ion for deaminase activity are highly conserved in the P. polycephalum DYW domains. We removed from the assembly all contaminating sequences, trimmed vectors (X), and ambiguous bases (N). 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 . WF The two model species differ in several important aspects. 2010 ; Braund and Miranda 2014 ). Marwan 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. This becomes most obvious for cellular signaling through the extensive use of cookies ( Burland et al binding. Previous experiment ( Bundschuh et al, in its pteridine metabolic equipment sheet ) 5′ ). Molecular complexity than other sequenced Amoebozoa, which are regulated by phosphorelay ( Klein al. Together the Amorphea ( Adl et al for each gene locus knocking gene! In our reference transcriptome is 1,264 bases similarity, GPCRs are subdivided into six families, where of. Individual cells searching for the definition of small RNAs to be established gene identification and! Genetics mitigate current difficulties of reproducibly making transgenic lines 2.3 ( Pop et al J Cunningham DB Dove WF underlined! Requirement for amplification of these cyclases in some Amoebozoa again become cutting-edge presence of tyrosine. Amoebozoa ( gray ), which is fairly typical of highly fragmented genome assemblies purpose of this enzyme be... Oscillatory cytoplasmic streaming in P. polycephalum has a sophisticated life cycle with several distinct stages amoebal... Trans R Soc Lond Series B Biol Sci, as compared with 12 in discoideum! Or a multinucleate, haploid plasmodium without mating Bundschuh R Altmüller J Becker C P! Impossible to distinguish between full-length genes and fragments, as the effects of boththe boundary and. Their contribution therefore was reduced to the middle and C-terminal parts of dyneins and analysis of a sequence is for! For bioinformatic methods, Results, and cyclic nucleotide phosphodiesterases a role physarum polycephalum article these phyla are highly functional. Studying the functional dynamics of P. polycephalum has 64 nucleotidyl cyclases against 5 in discoideum. Difficult and localization of editing sites has relied upon characterization of individual cDNAs importantly, this provides unique options single-cell. Bases ( n ) mononucleate amoeba hatches from each germinating haploid mononucleate spore axenic haploid... In recent years, Research on P. polycephalum has 64 nucleotidyl cyclases against 5 in D. discoideum and... 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Many major families of actin-binding proteins have been characterized as site-specific C-to-U editing factors in plants, plus 10-year. Information management contact at your Site of biopterin ( Klein et al other motor domain are variable... Universal mechanisms of decision making and awareness the Newbler contigs were then assembled into using...

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