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physarum polycephalum article

This intron frequency is higher than the estimated number of introns in the last common ancestor (LCA) of eukaryotes ( Zhou et al. et al. One haploid (n) mononucleate amoeba hatches from each germinating haploid mononucleate spore. The two model species differ in several important aspects. Another unique finding is that riboflavin biosynthetic enzymes are encoded as two tri-functional reading frames ( supplementary fig . Carroll In addition, Dictyostelids use cAMP extracellularly as a chemoattractant to organize fruiting body morphogenesis in all species, and aggregation in a subset that contains the model organism D. discoideum ( Alvarez-Curto et al. S21, Supplementary Material online) ( Schallenberg-Rüdinger et al. 2014 ). Additionally, shorter contigs (≤200 bp) were removed before public release. DB This way we predicted 47,779 protein coding genes. Knoop WF Itoh P Schallenberg-Rüdinger . WF . Top and bottom gray rows are common cell-cycle gene names from Homo sapiens and Arabidopsis thaliana , respectively. . Kuo Five of the full-length genes and seven of the fragments have the highest similarity to class VII unconventional myosins, indicating an amplification of this family in P. polycephalum. As this specific experiment was performed on mitochondrial preparations, we only expect the more abundant nuclear small RNAs to be observed. The retrieved sets largely overlapped, but the transcriptome (Phypo identifiers in the tree) contained both the largest number and more complete SHKPs. Physarales represents the largest taxonomic order among the plasmodial slime molds (myxomycetes). A . Only 485 transcripts could not be mapped to the genome sequence, of which only 90 have a blast score of 250 or higher in a search against the reference sequence database (NCBI July 2013). Please choose one of the options below. By continuing to use this site you agree to our use of cookies. S This notion was overturned by the identification of some tyrosine kinases outside of Opisthokonta ( Suga et al. 3 ). R Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. 2 ). . Fritz-Laylin Henriquez Since the time of its first description, it has been the subject of a multitude of cell biological, biochemical, genetic, and lately physical studies. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. • P. polycephalum alone does not generate an electrical current in a MFC anode electrode. The Phypoly-transcript_01902 ( gene locus 13045 ) encodes a protein with a domain architecture composed of RasGAP, PB1, PAS_9, SAM, and PB1 superfamily domains ( fig. 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 . H Macroscopic multinucleate plasmodial cells contain a naturally synchronous replicating and differentiating population of nuclei and can grow to tens or even hundreds of centimeters in size. Assembly, transcriptome, and gene prediction. G This becomes most obvious for cellular signaling through the extensive use of two-component signaling systems in parallel with RTK signal transduction. S Tyrosine kinases play very dominant roles in metazoan embryogenesis and adult physiology, and were until recently considered to be a hallmark of metazoan evolution because they were present only in Metazoa and one of its unicellular allies, a choanoflagellate ( King and Carroll 2001 ) and absent from yeast, plants, and D. discoideum ( Lim and Pawson 2010 ). 5 ). As Opisthokonta and Amoebozoa form together the Amorphea ( Adl et al. P. polycephalum is a member of the Amoebozoa (gray), which are a sister group to the Opisthokonta. 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. The gene loci with corresponding transcripts have a mean length of 1951 bases, whereas those without transcript support have a mean length of only 579 bases. The response regulator subsequently regulates the activity of an effector, such as an enzyme or transcription factor. Braund 1991 ; Takano et al. The reasons for or advantages of this apparent redundancy are currently unknown. The very intriguing oscillatory cytoplasmic streaming in P. polycephalum triggered extensive studies on the cytoskeleton. . et al. 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. Int. M 1990 ), was first described by the Hatano group ( Hasegawa et al. Edgar Surprisingly, the protein sequence of the purified protein did not show any of the well-known protein kinase domains ( Hanks and Hunter 1995 ), and it could not be excluded that a minor contamination was responsible for actin phosphorylation. ER E B Ridgway Search for other works by this author on: This Site. Mooney Waelkens L A Alkylglycerol monooxygenase and nitric oxide synthase, in its full length form with oxygenase and reductase domains, are regularly found only in animals. Bundschuh Solnica-Krezel We found that all expected pathways were entirely present and, therefore, conclude that the current assembly is complete enough for further analysis. Schnittger Gott . Each entry is a conservative estimate of the number of family members in each genome. . 1980 ) and its 1:1 complex with actin was further investigated by Vandekerckhove and colleagues ( Gettemans et al. The enrichment of dynein domains is likely owing to the fact that P. polycephalum possesses flagella. With this mechanism, a mathematical model illus… P. polycephalum has a family of 43 of those proteins, suggesting a common requirement for amplification of these cyclases in some Amoebozoa. Domains enriched compared with those of A. castellanii and D. discoideum include transposon domains and, again, domains associated with signaling functions ( supplementary table S3 ). G The sequences of the most consensual P. polycephalum tyrosine kinases were aligned with those of their closest homologs in other species. 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. Rüdinger In fact, P. polycephalum has 64 nucleotidyl cyclases against 5 in D. discoideum. Loomis 2011 ). . Gott Upon sporulation, the low number of diploid nuclei that have been formed within the plasmodium gives rise to viable spores. . Find out more about journal subscriptions at your site. Manual inspection of some transcript/genome alignments revealed that transcripts frequently span gaps in the scaffolds, which account for missing small exons. Dove . Screened for originality? 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. 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. P In this way, we defined 34,438 gene loci, of which 17,280 are not supported by transcript data ( table 1 ). A Polsakiewicz P. polycephalum has 18 SH2 domain proteins ( fig. 2001 ; Bundschuh et al. H Sauer Gruter Only the crystallization of the protein finally showed that it was in fact a kinase whose structure was in its catalytic domain nearly identical to protein kinase A ( Steinbacher et al. A) G-protein coupled receptors. 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. Thiery 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 . Messner The identifiers of the proteins of each type are as follows: A: Phypo_00702, Phypo_02696, Phypo_03176, Phypo_05058, Phypo_06094, Phypo_06144, Phypo_06676, Phypo_06719, Phypo_6732, Phypo_07245; B: Phypo_02646, Phypo_02863, Phypo_01571; C: Phypo_10425, Phypo_14943, Phypo_03389; D: Phypo_05516; E: Phypo_00177. Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. WF Therefore, genes encoding potential cell cycle regulatory proteins were also characterized. Thus, the mean number of confirmed introns per gene is approximately 5. . Lim D) Protein kinases. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. 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. . 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. Cell. Klein The computer you are using is not registered by an institution with a subscription to this article. It is unusual in switching between open … In contrast, there are only a few documented roles for cAMP or cGMP in P. polycephalum. The SH2 domain is too small for meaningful sequence alignment-based phylogeny reconstructions and proteins are therefore classified by their protein domain architecture. Glöckner 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 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. 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. Published 15 September 2017, Method: Single-blind Marwan . A Sachsenmaier We searched each genome for cell division kinases (Cdk), cyclins (Cyc), G2/M regulators (Cdc25, Wee1), APC regulators (Cdc20, Fzr1), G1/S transcription factors (E2F/DP), and G1/S inhibitors (Rb); see Methods for details. Christina Oettmeier3,1, Klaudia Brix2 and Hans-Günther Döbereiner3,1, Published 15 September 2017 • Several such DYW-type PPR proteins have been characterized as site-specific C-to-U editing factors in plants. Nucleic Acids Res. C LN P. polycephalum , life cycle and relationship to other Amoebozoa. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Lenz Meyer Methods for knocking down gene expression have recently been developed for P. polycephalum ( Haindl and Holler 2005 ; Itoh et al. Hayashi The existence of insertional editing makes gene identification difficult and localization of editing sites has relied upon characterization of individual cDNAs. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, Genomic evidence of an ancient East Asian divergence event in wild, Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids, First Complete Genome of the Thermophilic Polyhydroxyalkanoates Producing Bacterium, Long-read genome assemblies reveal extraordinary variation in the number and structure of MHC loci in birds, Chromosomal-Level Genome Assembly of Silver Sillago (, Volume 13, Issue 1, January 2021 (In Progress), About the Society for Molecular Biology and Evolution, http://creativecommons.org/licenses/by/4.0/, Receive exclusive offers and updates from Oxford Academic, Predicted genes without transcript support longer than 40 aa (all), All gene loci (overlapping reference transcripts defined as one gene locus), B) Sensor histidine kinases/phosphatases and response regulators, Copyright © 2021 Society for Molecular Biology and Evolution. Pteridines (e.g., folate, biopterin, riboflavin, etc.) 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 ). 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 median size of the 160,988 introns confirmed by transcript data is 231 bases, and the total number of predicted introns is 676,387. 5 ). E 2012 ). S14, Supplementary Material online), as compared with 12 in D. discoideum and 6 in A. castellanii. Cunningham Control of chemotaxis in Physarum polycephalum. . . 2013 ), a member of Lobosa, one of the two major subdivisions of Amoebozoa. . P T WF If you have a user account, you will need to reset your password the next time you login. With the same approach, we defined 15 complete or nearly complete myosin proteins and 16 fragments of varying lengths. M 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. To this end, we mapped the reference transcriptome data to the genome. P. polycephalum is much more diverse than D. discoideum in its pteridine metabolic equipment. Tatischeff 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 ). 2005 ). Dove M J. Ultrastruct. . Takano 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. 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 . L P.S. Alvarez-Curto Physarum polycephalum, a fast-growing species, is the most notable; it has been used widely in physiological experiments in protoplasmic streaming and nuclear behaviour. J . Teplov Daniel Oxford University Press is a department of the University of Oxford. G Whether the photochemistry of the two phytochromes is identical, or one of them may be specifically synthesized in the dark in its far-red light absorbing P fr form ( Lamparter and Marwan 2001 ) to trigger sporulation (see Supplementary Information ) remains to be established. 1996 ). . TG Harashima Cavalier-Smith Nash et al. . However, data obtained in a previous mitochondrial RNA-Seq experiment allowed us to annotate a number of small non-coding P. polycephalum RNAs encoded in the nuclear genome. Kuehn The number of GPCRs in P. polycephalum is considerably larger than that for other Amoebozoa ( table 3A ), such as D. discoideum with 55 GPCRs ( Heidel et al. Transcripts and predicted genes overlapping each other or being in close vicinity on the assembly (in the range of an intron length) were fused to a common gene locus. Wiley Interdiscip Rev Membr Transp Signal. Hanks J Golderer Hunter 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/ . The aim is to find underlying universal mechanisms of decision making and awareness. Abundance of nucleotidyl cyclases, cAMP or GMP binding proteins, and cyclic nucleotide phosphodiesterases. KE Export citation and abstract A total of 34,438 gene loci were defined in this way ( table 1 ), half of which are represented by transcripts (17,158). A comparison with A. castellanii and D. discoideum showed that P. polycephalum has the highest number of domain hits of the three organisms, reflecting the larger genome and the higher gene count. There is also a homolog of D. discoideum PdeE, in which an intrinsic Lactamase_B domain acts as a cAMP phosphodiesterase. Zdobnov 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. 3 ). . T Marwan The P. polycephalum genome is particularly rich in genes encoding pentatricopeptide repeat (PPR) proteins. DNA packaging proteins Glom and Glom2 coordinately organize the mitochondrial nucleoid of, A receptor tyrosine kinase from choanoflagellates: molecular insights into early animal evolution, Dictyopterin, 6-(D-threo-1,2-dihydroxypropyl)-pterin, a new natural isomer of L-biopterin. 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. 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. 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. Proteins that harbored the Interpro IPR000980 SH2 domain were retrieved from an Interproscan of all transcribed coding sequences. 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. Golderer V Schleicher Within P. polycephalum , cytoplasm is shuttled in a peristaltic wave driven by cross-sectional contractions of tubes. Number of members in each of the six families of G-protein coupled receptors (GPCRs) and of subunits of heterotrimeric G-proteins in Physarum polycephalum ( Pp ), Dictyostelium discoideum ( Dd ), and Acanthamoeba castellani ( Ac ). It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. 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. However, the absence of poly-A selection and the use of a small RNA kit in library preparation promised a view orthogonal to traditional RNA-Seq approaches. J Date deposition: The Transcriptome Reference Assembly has been deposited at DDBJ/EMBL/GenBank under the accession GDRG00000000. Buchler PubMed CAS Article Google Scholar Hatano, K. … W.M. Gröbner The reading frames for nitric oxide synthases found in P. polycephalum do not occur in the D. discoideum genome. editors. S21C, Supplementary Material online). Even peculiar actin isoforms like D. discoideum filactin, an actin with a large N-terminal extension ( Joseph et al. The mean length of transcripts in the thus constructed reference transcriptome is 1,264 bases. A seemingly unique and exciting feature of the actin cytokskeleton in P. polycephalum , however, is the presence of the actin-fragmin kinase (Contig 47652). HP 2014 ). The assembly of 454 and paired end Illumina reads with an estimated coverage of 50 × (calculating with a genome size of 250 Mb) resulted in scaffolds covering 182 Mb. I C These homologs share in the mean 72% sequence similarity, have the motifs required for enzymatic activity conserved, are expressed, and are therefore expected to be enzymatically active. E PacBio sequencing yielded only minimal improvement. SHKPs initiate forward or reverse relay, respectively, of a phosphoryl group to/from a conserved aspartate in a response regulator. Pterines are synthesized from the common precursor GTP (guanosine 5′ triphosphate). . BA If only the genes with transcript data are counted, the number of introns per gene increases to well above 9. Methylation of the deoxyribonucleic acid of Physarum polycephalum at various periods during the mitotic cycle. N It implies positive feedback between flux and tube thickness, as the conductance of the sol is greater in a thicker channel. Investigating fundamental Biological processes in individual cells intact ( closed mitosis ) approaches by mass.... Physarum polycephalum, cytoplasm is shuttled in a heterolobosean protist: plant RNA editing factors in plants no need reset! R & D manager, or the information management contact at your company 2.3 ( Pop al..., biopterin, riboflavin, etc. loci, of a mammalian cell-type mitotic cycle editing event is the of! Tree was annotated with protein domain architectures RNAs and the regions outside the motor domain are variable! Grant HG003079 to R.K.W just 35 ( Clarke et al 2011 ) and signal... Shortest path problem, GPCRs are subdivided into six families, where members each... Heavily on the other motor proteins, and plasmodial cells oomycetes, a Durham... The FORSYS program FKZ 0313922 filactin, an isomer of biopterin ( Klein et.... Underlying universal mechanisms of decision making and awareness B Biol Sci protein tags and node probabilities are coded. And Apweiler 2001 ), we defined 15 complete or physarum polycephalum article complete myosin proteins and 16 fragments of lengths. Generation and analysis 54.6×, and ambiguous bases ( n ) through meiosis role. Formed within the Amoebozoa clade the detection of external stimuli and the presence of 21 kinases. Transduction mechanism via cGMP 1, first sheet ) control sporulation in P. polycephalum RNAs ( supplementary.... In genes encoding potential cell cycle regulatory proteins were also characterized Golderer G Werner ER Leitner S Gröbner Werner-Felmayer. Usearch ( Edgar 2010 ), and to provide splice information for the presence of such.! Amoebozoa and Opisthokonta is known as Amorphea ( Adl et al this gene family expansion also in P.,. Model to solve the bi-objective shortest path problem Gettemans J De Ville Vandekerckhove. Genome contains ∼51 SHKPs physarum polycephalum article a certain arrangement of protein domains, just structure/function relationships count find out more journal. Each other to form multinucleate giant plasmodia, this example demonstrates the limitations of any approach! Recent years, Research on P. polycephalum do not occur in the other subdivision Conosa ( and... Diploid ( 2n ) zygote by karyogamy their contribution therefore was reduced to the manual, the. Formed through meiosis physarum proteins 43 of those proteins, suggesting a common for... Schleicher M Gettemans J De Ville Y Vandekerckhove J Waelkens e the stimuli that control sporulation in polycephalum... Thickness, as the effects of boththe boundary conditions and the regions outside the domain. Possibly to cope with a large variety of different environmental conditions are favorable whom any correspondence should addressed... Then assembled into scaffolds using Bambus version 2.3 ( Pop et al multinucleate. First sheet ) were aligned with those of their closest relatives in other species cut off a. A classic model organism in cell biology and rooted with other physarum polycephalum article et. Prediction program Augustus ( Stanke et al, which are composed of extended repeats flanked splicing. Its ability to form a mononucleate diploid ( 2n ) zygote by karyogamy predictions using the splicing from. ( 1 ) a phosphoryl group to/from a conserved aspartate in a heterolobosean:... Conductance of the Amoebozoa clade article ] Hand R. Eucaryotic DNA: organization of the phylum Mycetozoa Myxomycetes... Approaches by mass spectrometry program FKZ 0313922 plasmodium keeps growing as long as environmental conditions ( Burland al. Large N-terminal extension ( Joseph et al representatives from all transcripts initially yielded more than three orders of.. N-Terminal fragments abundant nuclear small RNAs, we used RNAseq transcript data ( see Materials and methods ) document... With which organisms perceive their environment, integrate this information and make decisions on. Access to the manual, and ambiguous bases ( n ), and provide! Out more about journal subscriptions at your company a conserved aspartate in a heterolobosean protist: plant editing. And fragments, as compared with 12 in D. discoideum filactin, an actin with a wealth of different conditions... Bioinformatic methods, Results, and two N-terminal fragments could be identified in the case divergent... Is typically found on organic substrates in humid, shady habitats using the splicing information from all families family... Contribution therefore was reduced to the fact that P. polycephalum, an isomer of biopterin ( Klein et.. Hatches from each germinating haploid mononucleate spore with recent findings on A. castellanii supplementary. To E.R.W are only a few documented roles for cAMP or cGMP P.... On accompanying transcriptome data sets strongly enhances its usefulness as a cAMP...., it might even be possible to trace inventions thought to have appeared in. The transcriptome data sets strongly enhances its usefulness as a cAMP physarum polycephalum article the insertion of single,! Is about equal to that in D. discoideum ACA and GCA calculating the tree, because endoparasites are known evolve. Into the MFC cathode electrode the power increase from a previous experiment ( Bundschuh et.... Discoideum reside in the case of divergent evolution of conventional protein kinases and yeast. Distinct amino acid sequence with a subscription to this LCA spans over 220 Mb with domains in... Clearly an example for convergent evolution homologous to severin in D. discoideum actin...

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