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Biochimica Et Biophysica Acta. General... Jun 2023Physarum polycephalum is an unusual macroscopic myxomycete expressing a large range of glycosyl hydrolases. Among them, enzymes from the GH18 family can hydrolyze...
BACKGROUND
Physarum polycephalum is an unusual macroscopic myxomycete expressing a large range of glycosyl hydrolases. Among them, enzymes from the GH18 family can hydrolyze chitin, an important structural component of the cell walls in fungi and in the exoskeleton of insects and crustaceans.
METHODS
Low stringency sequence signature search in transcriptomes was used to identify GH18 sequences related to chitinases. Identified sequences were expressed in E. coli and corresponding structures modelled. Synthetic substrates and in some cases colloidal chitin were used to characterize activities.
RESULTS
Catalytically functional hits were sorted and their predicted structures compared. All share the TIM barrel structure of the GH18 chitinase catalytic domain, optionally fused to binding motifs, such as CBM50, CBM18, and CBM14, involved in sugar recognition. Assessment of the enzymatic activities following deletion of the C-terminal CBM14 domain of the most active clone evidenced a significant contribution of this extension to the chitinase activity. A classification based on module organization, functional and structural criteria of characterized enzymes was proposed.
CONCLUSIONS
Physarum polycephalum sequences encompassing a chitinase like GH18 signature share a modular structure involving a structurally conserved catalytic TIM barrels decorated or not by a chitin insertion domain and optionally surrounded by additional sugar binding domains. One of them plays a clear role in enhancing activities toward natural chitin.
GENERAL SIGNIFICANCE
Myxomycete enzymes are currently poorly characterized and constitute a potential source for new catalysts. Among them glycosyl hydrolases have a strong potential for valorization of industrial waste as well as in therapeutic field.
Topics: Chitinases; Physarum polycephalum; Myxomycetes; Escherichia coli; Chitin; Sugars
PubMed: 36933625
DOI: 10.1016/j.bbagen.2023.130343 -
ELife Mar 2023Veins in vascular networks, such as in blood vasculature or leaf networks, continuously reorganize, grow or shrink, to minimize energy dissipation. Flow shear stress on...
Veins in vascular networks, such as in blood vasculature or leaf networks, continuously reorganize, grow or shrink, to minimize energy dissipation. Flow shear stress on vein walls has been set forth as the local driver for a vein's continuous adaptation. Yet, shear feedback alone cannot account for the observed diversity of vein dynamics - a puzzle made harder by scarce spatiotemporal data. Here, we resolve network-wide vein dynamics and shear rate during spontaneous reorganization in the prototypical vascular networks of . Our experiments reveal a plethora of vein dynamics (stable, growing, shrinking) where the role of shear is ambiguous. Quantitative analysis of our data reveals that (a) shear rate indeed feeds back on vein radius, yet, with a time delay of 1-3 min. Further, we reconcile the experimentally observed disparate vein fates by developing a model for vein adaptation within a network and accounting for the observed time delay. The model reveals that (b) vein fate is determined by parameters - local pressure or relative vein resistance - which integrate the entire network's architecture, as they result from global conservation of fluid volume. Finally, we observe avalanches of network reorganization events that cause entire clusters of veins to vanish. Such avalanches are consistent with network architecture integrating parameters governing vein fate as vein connections continuously change. As the network architecture integrating parameters intrinsically arise from laminar fluid flow in veins, we expect our findings to play a role across flow-based vascular networks.
Topics: Veins; Physarum polycephalum
PubMed: 36916885
DOI: 10.7554/eLife.78100 -
Mycologia 2023The noncellular complex structures of fruiting body produced by a multinucleate large plasmodium are the distinct character of Myxomycetes. Although the fruiting body...
The noncellular complex structures of fruiting body produced by a multinucleate large plasmodium are the distinct character of Myxomycetes. Although the fruiting body distinguishes myxomycetes from other amoeboid single-cell organisms, it is unclear how such complex structures arise out of a single cell. The present study investigated the detailed process of fruiting body formation in , the type species of the genus , at the cellular level. A single cell excretes cellular waste and excess water during the formation of the fruiting body by controlling its shape, secreted materials, and organelle distribution. These excretion phenomena lead to the morphology of the mature fruiting body. The results of this study suggest that the structures of the fruiting body are involved not merely in spore dispersal but also in the process of dehydration and self-cell cleaning of the single cell for the next generation.
Topics: Humans; Myxomycetes; Dehydration
PubMed: 36877890
DOI: 10.1080/00275514.2023.2170146 -
Mycologia 2023Despite various attempts during the last few decades to establish a natural system for the Myxomycetes, researchers have not yet reached a consensus. One of the most...
Despite various attempts during the last few decades to establish a natural system for the Myxomycetes, researchers have not yet reached a consensus. One of the most drastic recent proposals is the movement of the genus , an almost a trans-subclass transfer. The traditional subclasses are not supported by current molecular phylogenies, and various higher classifications have been proposed during the last decade. However, the taxonomic characteristics on which the traditional higher classifications were based have not been reinvestigated. In the present study, the key species involved in this transfer, (the type species of the genus ), was assessed using correlational morphological analysis of stereo, light, and electron microscopic images. Correlational analysis of the plasmodium, fruiting body formation, and the mature fruiting bodies revealed that several concepts of taxonomic characteristics that have been used to distinguish higher classifications are questionable. The results of this study indicate that caution is required when interpreting the evolution of morphological traits in Myxomycetes, as the current concepts are vague. The definitions of the taxonomic characteristics need a detailed research, and attention should be paid to the lifecycle timing of observations, before discussing a natural system for Myxomycetes.
Topics: Myxomycetes; Phylogeny; Reproduction
PubMed: 36867578
DOI: 10.1080/00275514.2023.2170144 -
Philosophical Transactions of the Royal... Apr 2023Changes in behaviour over the lifetime of single-cell organisms have primarily been investigated in response to environmental stressors. However, growing evidence...
Changes in behaviour over the lifetime of single-cell organisms have primarily been investigated in response to environmental stressors. However, growing evidence suggests that unicellular organisms undergo behavioural changes throughout their lifetime independently of the external environment. Here we studied how behavioural performances across different tasks vary with age in the acellular slime mould . We tested slime moulds aged from 1 week to 100 weeks. First, we showed that migration speed decreases with age in favourable and adverse environments. Second, we showed that decision making and learning abilities do not deteriorate with age. Third, we revealed that old slime moulds can recover temporarily their behavioural performances if they go throughout a dormant stage or if they fuse with a young congener. Last, we observed the response of slime mould facing a choice between cues released by clone mates of different age. We found that both old and young slime moulds are attracted preferentially toward cues left by young slime moulds. Although many studies have studied behaviour in unicellular organisms, few have taken the step of looking for changes in behaviour over the lifetime of individuals. This study extends our knowledge of the behavioural plasticity of single-celled organisms and establishes slime moulds as a promising model to investigate the effect of ageing on behaviour at the cellular level. This article is part of a discussion meeting issue 'Collective behaviour through time'.
Topics: Humans; Infant, Newborn; Physarum polycephalum; Learning; Cues
PubMed: 36802777
DOI: 10.1098/rstb.2022.0063 -
Biology Letters Feb 2023In metazoans, the expression of key phenotypic traits is sensitive to two- and three-way interactions between variation in mitochondrial DNA, nuclear DNA and the...
In metazoans, the expression of key phenotypic traits is sensitive to two- and three-way interactions between variation in mitochondrial DNA, nuclear DNA and the external environment. Whether gene--environment interactions affect phenotypes in single-celled eukaryotes is poorly studied, except in a few species of yeast and fungi. We developed a genetic panel of the unicellular slime mould, containing strains differing in mitochondrial and nuclear DNA haplotypes. The panel also included two strains harbouring a selfishly replicating mitochondrial-fusion (mF) plasmid that could affect phenotype expression. We assayed movement and growth rate differences among the strains across two temperature regimes: 24° and 28°C. We found that the slime mould's growth rate, but not movement, is affected by G × G × E interactions. Predictably, mtDNA × nDNA interactions significantly affected both traits. The inter-trait correlation across the strains in each temperature regime was positive. Surprisingly, the mF plasmid had no negative effects on our chosen traits. Our study is the first to demonstrate genetic regulation of phenotype expression in a unicellular slime mould. The genetic effect on phenotypes manifests via epistatic interactions with the thermal environment, thus shedding new light on the role of G × G × E interactions in trait evolution in protists.
Topics: Physarum polycephalum; DNA, Mitochondrial; Mitochondria; Plasmids; Phenotype
PubMed: 36789533
DOI: 10.1098/rsbl.2022.0494 -
International Journal of Molecular... Jan 2023The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone...
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. 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 . However, histone chaperones differ significantly between animal and plant kingdoms, and this thus probed us to further study the conservation of histone chaperones in 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. 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 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.
Topics: Animals; Histones; Physarum polycephalum; Histone Chaperones; Saccharomyces cerevisiae; Chromatin; Molecular Chaperones
PubMed: 36674565
DOI: 10.3390/ijms24021051 -
Journal of Natural Products Mar 2023The myxomycete , colloquially referred to as "dog vomit fungus", forms vibrant yellow fruiting bodies (aethalia) on wood chips during warm and humid conditions in...
The myxomycete , colloquially referred to as "dog vomit fungus", forms vibrant yellow fruiting bodies (aethalia) on wood chips during warm and humid conditions in spring. In 2018, ideal climatic conditions in Sydney, Australia, provided a rare opportunity to access abundant quantities of aethalia, which enabled the isolation, purification, structure elucidation, and biological screening of two avenalumamide pyrones, fuligopyrone () and fuligopyrone B (). While and did not exhibit any appreciable biological activity, their significant UV absorption at 325 nm suggested they may be acting as transient sunscreens to help protect the fruiting mass from exposure to sunlight. In support of this hypothesis, exposing a solution of to direct sunlight for 5 min resulted in rapid equilibration with a mixture of 2,4-fuligopyrone B () and 2,4-fuligopyrone B () photoisomers.
Topics: Animals; Dogs; Myxomycetes; Ultraviolet Rays; Ascomycota; Fruiting Bodies, Fungal; Australia
PubMed: 36655352
DOI: 10.1021/acs.jnatprod.2c00989 -
Plant Disease Jan 2023(Dicks.) Gray, named "Maitake" in Japan, is mainly cultivated in China, Japan and Korea as a rare delicacy (Park et al. 2015). is a medicinal and edible mushroom that...
(Dicks.) Gray, named "Maitake" in Japan, is mainly cultivated in China, Japan and Korea as a rare delicacy (Park et al. 2015). is a medicinal and edible mushroom that can enhance the human immunology system. In recent years, the production of has increased in China due to its high economic value and as a source of livelihood for small scale farmers. From August to September 2017, a serious slime mold disease was observed on G. frondosa under greenhouse conditions in Qingyuan County, Lishui city, Zhejiang Province, China. Incidence was 10 to 30% in most surveyed mushroom greenhouses, sometimes more than 80% in mushroom greenhouses without proper management. The disease reduced production by 10% on average, and over 80% in severe cases. Slime mold disease usually appeared after irrigation, the kelly plasmodia migrate firstly from the root of fruiting body to stem and finally to pileus, then the infected parts became soft and putrid with slime on the surface. Additionally, many other organisms grow on decayed fruiting bodies, such as bacteria, fungi, and insects. The disease can spread rapidly through soil to adjacent fruiting bodies resulting in yield reduction. Samples were collected and cultures were isolated by transferring diseased fruiting bodies with yellow green plasmodia onto 2% water agar medium. Plasmodia were purified through aseptically transferring their edge segment to a new sterile 2% water agar medium, and this procedure was repeated three or four times to free the isolate from contaminating organisms. Purified plasmodia were then placed on the solid bacteriological test medium (SGM), containing glucose, peptone, yeast extract, mineral salts and hematin used in the axenic culture of (Daniel et al. 1964), to verify bacteria presence. Plasmodia were also induced to form sporocarps. Voucher specimens were deposited in the Fungarium of Jiangxi Academy of Agricultural Sciences (FJAAS-M0001) and the Herbarium of the Mycology, Engineering Research Center of Edible and Medicinal Fungi, Chinese Ministry of Education, Jilin Agricultural University (HMJAU-M1561). Sporocarps were stalked, globose to discoid, golden-yellow, 0.9-1.8 mm in height, 0.28-0.55 mm in diameter. Hypothallus was small, thin, orange. Stalks were subulated, about twice to thrice the diameter of the sporotheca, bright orange below, yellow above, furrowed. Peridium was weak, thin, and plated with yellow calcareous flakes. Capillitium was a small meshed, persistent net of tubules with small and yellow angular lime nodes. Spores were globose, free, dark brown to black in mass, purplish brown in transmitted light, 8-10 μm in diameter, smooth under light microscopy. Irregular spinulose spores showed clusters of small warts that are conspicuous under scanning electron microscopy. Plasmodia were yellow green. The 18S ribosomal RNA gene was amplified with primer SMNUR101/NS4 (Rusk et al. 1995; White et al. 1990). The 18S rRNA gene sequence was submitted to GenBank (OP373728) and an 18S rRNA gene phylogenetic tree of Physarum obtained by maximum likelihood analysis (ML) and Bayesian inferences (BI) of 23 taxa and 1,608 aligned positions was produced. Based on sporocarps morphological characteristics, plasmodial cultural traits, and the sequence of 18S rRNA, the slime mold was identified as . A pathogenicity test was performed by gently inoculating a 12 mm diameter circinal patch of SGM with plasmodia on three healthy fruiting bodies of G. frondosa. All treatments were cultured in a mushroom-growing room with temperature 24 to 29 ℃ and relative humidity of 87 to 96%. Three fruiting bodies inoculated with a 12 mm diameter SGM served as controls. All fruiting bodies inoculated with plasmodia showed the same symptom. No symptoms developed on the controls. The pathogen was consistently reisolated from the symptomatic fruiting bodies of and confirmed to be based on cultural, morphological and molecular characteristics, thus fulfilling Kock's postulates. This is the first report of causing yellow rot disease on cultivated . References: Daniel, J. W., et al. 1964. Page 9 in: Methods in Cell Biology. Academic Press, New York. Denchev, C. M. 2008. Mycologia Balc. 5:93. Park, H. S., et al. 2015. Biosci., biotechnol., and biochem. 79:147. Rusk, S. A., et al. 1995. Mycologia. 87:140. White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA.
PubMed: 36627806
DOI: 10.1094/PDIS-10-22-2419-PDN -
BMC Microbiology Dec 2022Myxomycetes are a group of eukaryotes belonging to Amoebozoa, which are characterized by a distinctive life cycle, including the plasmodium stage and fruit body stage....
BACKGROUND
Myxomycetes are a group of eukaryotes belonging to Amoebozoa, which are characterized by a distinctive life cycle, including the plasmodium stage and fruit body stage. Plasmodia are all found to be associated with bacteria. However, the information about bacteria diversity and composition in different plasmodia was limited. Therefore, this study aimed to investigate the bacterial diversity of plasmodia from different myxomycetes species and reveal the potential function of plasmodia-associated bacterial communities.
RESULTS
The bacterial communities associated with the plasmodia of six myxomycetes (Didymium iridis, Didymium squamulosum, Diderma hemisphaericum, Lepidoderma tigrinum, Fuligo leviderma, and Physarum melleum) were identified by 16S rRNA amplicon sequencing. The six plasmodia harbored 38 to 52 bacterial operational taxonomic units (OTUs) that belonged to 7 phyla, 16 classes, 23 orders, 40 families, and 53 genera. The dominant phyla were Bacteroidetes, Firmicutes, and Proteobacteria. Most OTUs were shared among the six myxomycetes, while unique bacteria in each species only accounted for a tiny proportion of the total OTUs.
CONCLUSIONS
Although each of the six myxomycetes plasmodia had different bacterial community compositions, a high similarity was observed in the plasmodia-associated bacterial communities' functional composition. The high enrichment for gram-negative (> 90%) and aerobic (> 99%) bacteria in plasmodia suggest that myxomycetes may positively recruit certain kinds of bacteria from the surrounding environment.
Topics: Humans; Myxomycetes; RNA, Ribosomal, 16S; Physarum; Bacteria; Plasmodium
PubMed: 36544088
DOI: 10.1186/s12866-022-02725-5