Origin and evolution of the slime molds (Mycetozoa)

Biochemical characterization of a unique cytokinin and nucleotide phosphoribohydrolase Lonely Guy protein from Dictyostelium discoideum

Lonely guy (LOG) proteins are phosphoribohydrolases (PRHs) that are key cytokinin (CK)-activating enzymes in plant and non-plant CK-producing organisms. During CK biosynthesis, LOGs catalyze the conversion of precursor CK-nucleotides (CK-NTs) to biologically active free base forms. LOG/PRH activity has been detected in bacteria, archaea, algae, and fungi. However, in these organisms, the LOG/PRH activity for CK-NTs and non-CK-NTs (e.g., adenine-NTs) has not been assessed simultaneously, which leaves limited knowledge about the substrate specificity of LOGs. Thus, we performed bioinformatic analyses and a biochemical characterization of a LOG ortholog from Dictyostelium discoideum, a soil-dwelling amoeba, which produces CKs during unicellular growth and multicellular development. We show that DdLog exhibits LOG/PRH activity on two CK-NTs, N 6 -isopentenyladenosine-5'-monophosphate (iPMP) and N 6 -benzyladenosine-5'-monophosphate (BAMP), and on adenosine 5'-monophosphate (AMP) but not on 3', 5'-cyclic adenosine-monophosphate (cAMP). Additionally, there were higher turnover rates for CK-NTs over AMP. Together, these findings confirm that DdLog acts as a CK-activating enzyme; however, in contrast to plant LOGs, it maintains a wider specificity for other substrates (e.g., AMP) reflecting it has maintained its original, non-CK related role even after diversifying into a CK-activating enzyme.

Exploring discrete space-time models for information transfer: Analogies from mycelial networks to the cosmic web

Fungal mycelium networks are large scale biological networks along which nutrients, metabolites flow. Recently, we discovered a rich spectrum of electrical activity in mycelium networks, including action-potential spikes and trains of spikes. Reasoning by analogy with animals and plants, where travelling patterns of electrical activity perform integrative and communicative mechanisms, we speculated that waves of electrical activity transfer information in mycelium networks. Using a new discrete space-time model with emergent radial spanning-tree topology, hypothetically comparable mycelial morphology and physically comparable information transfer, we provide physical arguments for the use of such a model, and by considering growing mycelium network by analogy with growing network of matter in the cosmic web, we develop mathematical models and theoretical concepts to characterise the parameters of the information transfer.

Unraveling the distribution pattern and driving forces of soil microorganisms under geographic barriers

The Altai Mountains (ALE) and the Greater Khingan Mountains (GKM) in northern China are forest regions dominated by coniferous trees. These geographically isolated regions provide an ideal setting for studying microbial biogeographic patterns. In this study, we employed high-throughput techniques to obtain DNA sequences of soil myxomycetes, bacteria, and fungi and explored the mechanisms underlying the assembly of both local and cross-regional microbial communities in relation to environmental factors. Our investigation revealed that the environmental heterogeneity in ALE and GKM significantly affected the succession and assembly of soil bacterial communities at cross-regional scales. Specifically, the optimal environmental factors affecting bacterial Bray-Curtis similarity were elevation and temperature seasonality. The spatial factors and climate change impact on bacterial communities under the geographical barriers surpassed that of local soil microenvironments. The assembly pattern of bacterial communities transitions from local drift to cross-regional heterogeneous selection. Environmental factors had a relatively weak influence on myxomycetes and fungi. Both soil myxomycetes and fungi faced considerable dispersal limitation at local and cross-regional scales, ultimately leading to weak geographical distribution patterns.IMPORTANCEThe impact of environmental selection and dispersal on the soil microbial spatial distribution is a key concern in microbial biogeography, particularly in large-scale geographical patterns. However, our current understanding remains limited. Our study found that soil bacteria displayed a distinct cross-regional geographical distribution pattern, primarily influenced by environmental selection. Conversely, the cross-regional geographical distribution patterns of soil myxomycetes and fungi were relatively weak. Their composition exhibited a weak association with the environment at local and cross-regional scales, with assembly primarily driven by dispersal limitation.

Distribution, assembly, and interactions of soil microorganisms in the bright coniferous forest area of China's cold temperate zone

The bright coniferous forest area in the cold temperate zone of China is a terrestrial ecosystem primarily dominated by low mountain Larix gmelinii trees. Limited information is available regarding the assembly mechanisms and interactions of microbial communities in the soil in this region. This study employed high-throughput techniques to obtain DNA from myxomycetes, bacteria, and fungi in the soil, evaluated their diversity in conjunction with environmental factors, associated them with the assembly process, and explored the potential interaction relationships between these microorganisms. The findings of our study showed that environmental factors had a more significant influence on the α and β diversity of bacteria compared to myxomycetes and fungi. Microbial communities were influenced by environmental selection and geographical diffusion, although environmental selection appeared to have a more significant impact than geographical diffusion. Our study suggested that different microorganisms exhibited unique evolutionary patterns and may have different assembly modes within phylogenetic groups. Myxomycetes and fungi exhibited a similar assembly process that was mainly influenced by stochastic dispersal limitation and drift. In contrast, bacteria's assembly process was primarily influenced by stochastic drift and deterministic homogeneous selection. The community of myxomycetes and fungi is greatly influenced by spatial distribution and random events, while bacteria have a relatively stable population composition in specific regions and may also be subject to environmental constraints. Finally, this study revealed that Humicolopsis cephalosporioides, a fungus that exclusively resided in cold environments, may play a critical role as a keystone species in maintaining molecular ecological networks and was considered a core member of the microbiome.

Multigene phylogeny of the order Physarales (Myxomycetes, Amoebozoa): shedding light on the dark-spored clade

The class Myxomycetes consists of free-living protists characterised by their complex life cycle, which includes both microscopic (amoebae, flagellates and cists) and macroscopic stages (spore-bearing fruiting bodies, sclerotia, and plasmodia). Within it, the order Physarales, with more than 450 recognised species, constitutes the largest group. Although previous studies have shown the polyphyly of some of the traditionally accepted genera, its internal phylogenetic relationships have remained uncertain so far, and together with the lack of data for some key species, it prevented any taxonomic and nomenclatural revisions. We have compiled a substantially expanded dataset in terms of both taxon sampling and molecular data, including most of the genera described to date and four unlinked DNA regions, for which we provide partial sequences: nSSU, EF-1α, α-Tub, and mtSSU, analysed through maximum likelihood and Bayesian methods. Our results confirm that the family Didymiaceae is paraphyletic to the rest of Physarales. Within Didymiaceae s.lat., the recent reinstatement of the genus Polyschismium for most species traditionally ascribed to Lepidoderma, except for the type (Ronikier et al. 2022), is further supported here, as well as the definite inclusion of the genus Mucilago in Didymium and Lepidoderma s.str. (L. tigrinum) in Diderma (Prikhodko et al. 2023). Additionally, the genus Diachea is redefined to include some species previously treated in Physaraceae (Craterium spp. with true columella). Within the monophyletic family Physaraceae, most genera are recovered as polyphyletic, suggesting that they should be no longer accepted as currently defined. However, the lack of resolution of some relationships within Physaraceae prevents us from resuscitating or creating several new genera to mitigate polyphyly. Among the well-defined groups with clear molecular signatures, we propose two taxonomic and nomenclatural changes at generic level: 1) a new genus, Nannengaella, is proposed for a major clade containing Physarum globuliferum and other species with heavily calcified sporophores and, often, a true calcareous columella; 2) Lignydium is resurrected for the clade containing Fuligo muscorum. Additionally, Trichamphora is suggested as the correct name for the clade containing Physarum pezizoideum. The taxonomy and nomenclature of some provisional genera, currently synonymous with Fuligo and Physarum, are disentangled, and we provide a comprehensive and updated nomenclatural conspectus that can be used when better resolved phylogenies are obtained. In total, 22 new combinations are proposed in different genera. A provisional key to the genera of the order is also provided. Citation: García-Martín JM, Zamora JC, Lado C. 2023. Multigene phylogeny of the order Physarales (Myxomycetes, Amoebozoa): shedding light on the dark-spored clade. Persoonia 51: 89-124. doi: 10.3767/persoonia.2023.51.02.

Dictyostelium discoideum cells retain nutrients when the cells are about to overgrow their food source

Dictyostelium discoideum is a unicellular eukaryote that eats bacteria, and eventually outgrows the bacteria. D. discoideum cells accumulate extracellular polyphosphate (polyP), and the polyP concentration increases as the local cell density increases. At high cell densities, the correspondingly high extracellular polyP concentrations allow cells to sense that they are about to outgrow their food supply and starve, causing the D. discoideum cells to inhibit their proliferation. In this report, we show that high extracellular polyP inhibits exocytosis of undigested or partially digested nutrients. PolyP decreases plasma membrane recycling and apparent cell membrane fluidity, and this requires the G protein-coupled polyP receptor GrlD, the polyphosphate kinase Ppk1 and the inositol hexakisphosphate kinase I6kA. PolyP alters protein contents in detergent-insoluble crude cytoskeletons, but does not significantly affect random cell motility, cell speed or F-actin levels. Together, these data suggest that D. discoideum cells use polyP as a signal to sense their local cell density and reduce cell membrane fluidity and membrane recycling, perhaps as a mechanism to retain ingested food when the cells are about to starve.

This article has an associated First Person interview with the first author of the paper.

<i>Lamproderma vietnamense</i>: a new species of myxomycetes with reticulate spores from Phia Oắc - Phia Đén National Park (northern Vietnam) supported by molecular phylogeny and morphological analysis

A new species of Lamproderma (Myxomycetes), described herein as L. vietnamense, was recovered in the field on ground litter from mountain subtropical forests (Phia Oắc - Phia Đén National Park) of northern Vietnam. Morphological details were examined by light and scanning electron microscopy. The species is characterized by a distinct and unique combination of morphological features, including a bright blue, shiny and very thin membranous peridium, a small dome-shaped columella, rigid, straight, branched, brown capillitial threads which gradually become pale at the periphery and finally colorless at the tips and small-meshed, banded-reticulate spores with 9-12 meshes across the spore diameter and solid walls without perforations 0.3-0.5 µm high. The stability of the taxonomic characters of L. vietnamense is supported by two well-developed collections found in 2018 and 2019. Partial sequences of three molecular markers (SSU, EF1α, COI) for both collections are identical. A two-gene phylogeny of the first two markers displays the two known accessions as a well-separated entity and indicates affinity of the new species with L. columbinum (the type taxon of the genus), L. violaceum, and several nivicolous Lamproderma species.

Generation of a mitochondrial protein compendium in Dictyostelium discoideum

The social ameba Dictyostelium discoideum has emerged as a powerful model to study mitochondrial genetics and bioenergetics. However, a comprehensive inventory of mitochondrial proteins that is critical to understanding mitochondrial processes has yet to be curated. Here, we utilized high-throughput multiplexed protein quantitation and homology analyses to generate a high-confidence mitochondrial protein compendium consisting of 936 proteins. Our proteomic approach, which utilizes mass spectrometry in combination with mathematical modeling, was validated through mitochondrial targeting sequence prediction and live-cell imaging. Our final compendium consists of 936 proteins. Nearly, a third of D. discoideum mitochondrial proteins do not have homologs in humans, budding yeasts, or an ancestral alphaproteobacteria. Additionally, we leverage our compendium to highlight the complexity of metabolic reprogramming during starvation-induced development. Our compendium lays a foundation to investigate mitochondrial processes that are unique in ameba and to understand the functions of conserved mitochondrial proteins in D. discoideum.

Cytopathological Outcomes of Knocking Down Expression of Mitochondrial Complex II Subunits in Dictyostelium discoideum

Mitochondrial Complex II is composed of four core subunits and mutations to any of the subunits result in lowered Complex II activity. Surprisingly, although mutations in any of the subunits can yield similar clinical outcomes, there are distinct differences in the patterns of clinical disease most commonly associated with mutations in different subunits. Thus, mutations to the SdhA subunit most often result in mitochondrial disease phenotypes, whilst mutations to the other subunits SdhB-D more commonly result in tumour formation. The reason the clinical outcomes are so different is unknown. Here, we individually antisense-inhibited three of the Complex II subunits, SdhA, SdhB or SdhC, in the simple model organism Dictyostelium discoideum. Whilst SdhB and SdhC knockdown resulted in growth defects on bacterial lawns, antisense inhibition of SdhA expression resulted in a different pattern of phenotypic defects, including impairments of growth in liquid medium, enhanced intracellular proliferation of the bacterial pathogen Legionella pneumophila and phagocytosis. Knockdown of the individual subunits also produced different abnormalities in mitochondrial function with only SdhA knockdown resulting in broad mitochondrial dysfunction. Furthermore, these defects were shown to be mediated by the chronic activation of the cellular energy sensor AMP-activated protein kinase. Our results are in agreement with a role for loss of function of SdhA but not the other Complex II subunits in impairing mitochondrial oxidative phosphorylation and they suggest a role for AMP-activated protein kinase in mediating the cytopathological outcomes.

Identification and characterization of histones in Physarum polycephalum evidence a phylogenetic vicinity of Mycetozoans to the animal kingdom

Physarum polycephalum belongs to Mycetozoans, a phylogenetic clade apart from the animal, plant and fungus kingdoms. Histones are nuclear proteins involved in genome organization and regulation and are among the most evolutionary conserved proteins within eukaryotes. Therefore, this raises the question of their conservation in Physarum and the position of this organism within the eukaryotic phylogenic tree based on histone sequences. We carried out a comprehensive study of histones in Physarum polycephalum using genomic, transcriptomic and molecular data. Our results allowed to identify the different isoforms of the core histones H2A, H2B, H3 and H4 which exhibit strong conservation of amino acid residues previously identified as subject to post-translational modifications. Furthermore, we also identified the linker histone H1, the most divergent histone, and characterized a large number of its PTMs by mass spectrometry. We also performed an in-depth investigation of histone genes and transcript structures. Histone proteins are highly conserved in Physarum and their characterization will contribute to a better understanding of the polyphyletic Mycetozoan group. Our data reinforce that P. polycephalum is evolutionary closer to animals than plants and located at the crown of the eukaryotic tree. Our study provides new insights in the evolutionary history of Physarum and eukaryote lineages.

Evolution and origin of sliding clamp in bacteria, archaea and eukarya

The replication of DNA is an essential process in all domains of life. A protein often involved in replication is the sliding clamp. The sliding clamp encircles the DNA and helps replicative polymerase stay attached to the replication machinery increasing the processivity of the polymerase. In eukaryotes and archaea, the sliding clamp is called the Proliferating Cell Nuclear Antigen (PCNA) and consists of two domains. This PCNA forms a trimer encircling the DNA as a hexamer. In bacteria, the structure of the sliding clamp is highly conserved, but the protein itself, called beta clamp, contains three domains, which dimerize to form a hexamer. The bulk of literature touts a conservation of the structure of the sliding clamp, but fails to recognize the conservation of protein sequence among sliding clamps. In this paper, we have used PSI blast to the second iteration in NCBI to show a statistically significant sequence homology between Pyrococcus furiosus PCNA and Kallipyga gabonensis beta clamp. The last two domains of beta clamp align with the two domains of PCNA. This homology data demonstrates that PCNA and beta clamp arose from a common ancestor. In this paper, we have further used beta clamp and PCNA sequences from diverse bacteria, archaea and eukarya to build maximum likelihood phylogenetic tree. Most, but not all, species in different domains of life harbor one sliding clamp from vertical inheritance. Some of these species that have two or more sliding clamps have acquired them from gene duplication or horizontal gene transfer events.

The evolution of convex trade-offs enables the transition towards multicellularity

The evolutionary transition towards multicellular life often involves growth in groups of undifferentiated cells followed by differentiation into soma and germ-like cells. Theory predicts that germ soma differentiation is facilitated by a convex trade-off between survival and reproduction. However, this has never been tested and these transitions remain poorly understood at the ecological and genetic level. Here, we study the evolution of cell groups in ten isogenic lines of the unicellular green algae Chlamydomonas reinhardtii with prolonged exposure to a rotifer predator. We confirm that growth in cell groups is heritable and characterized by a convex trade-off curve between reproduction and survival. Identical mutations evolve in all cell group isolates; these are linked to survival and reducing associated cell costs. Overall, we show that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.

Multicellularity is a major evolutionary transition that remains poorly characterized at the ecological and genetic level. Exposing unicellular green algae to a rotifer predator showed that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.

Design of potentially universal SSU primers in myxomycetes using next-generation sequencing

Unlike fungi, which have a universally accepted barcode marker, universal primers still lack in myxomycetes. Typically, DNA barcode primers were designed based on comparing existing myxomycetes sequences and targeting the conserved regions. However, the extreme genetic diversity within major myxomycetes groups and the frequent occurrence of group I introns have made the development of universal DNA barcode a severe challenge. The emergence of next-generation sequencing provides an opportunity to address this problem. We sequenced the mixed genomic DNA of 81 myxomycetes and extracted the SSU gene's reads using next-generation sequencing. After alignment and assembly, we designed a set of SSU primers that matched all potential SNPs, avoided all known group I intron insertion sites, and were highly conserved between major myxomycetes orders. This set of SSU primers has the potential to become one of the universal primer combinations. Due to the high genetic divergence caused by long and complicated evolutionary histories, the lack of universal barcode primers is common in protists. Our research provides a new method to solve this problem.

Comparative modelling unravels the structural features of eukaryotic TCTP implicated in its multifunctional properties: an in silico approach

Comparative modelling helps compare the structure and functions of a given protein, to track the path of its origin and evolution and also guide in structure-based drug discovery. Presently, this has been applied for modelling the tertiary structure of highly conserved eukaryotic TCTP (translationally controlled tumour protein) which is involved in a plethora of functions during growth and development and also acts as a biomarker for many cancers like lung, breast, and prostate cancer. The modelled TCTP structures of different organisms belonging to the eukaryotic group showed similar spatial arrangement of structural units except loops and similar patterns of root mean square deviation (RMSD), root mean square fluctuation, and radius of gyration (Rg) inspected through molecular dynamics simulations. Essential dynamics (ED) analyses revealed different domains that exhibited different motions for the assistance in its multifunctional properties. Construction of a free-energy landscape (FEL) based on Rg versus RMSD was employed to characterize the folding behaviours of structures and observe that all proteins had nearly similar conformation and topologies, indicating common thermodynamic/kinetic pathways. A physico-chemical interaction study demonstrated the helices and sheets were well stabilized with ample amounts of bonding compared to turns or loops and charged residues were more accessible to solvent molecules. Hence, the current study reveals the important structural features of TCTP that aid in diverse functions in a wide range of organisms, thus extending our knowledge of TCTP and also providing a venue for designing the potent inhibitors against it.

Amoeboid protist systematics: A report on the "Systematics of amoeboid protists" symposium at the VIIIth ECOP/ISOP meeting in Rome, 2019

Amoeboid protists are extremely abundant and diverse in natural systems where they often play outstanding ecological roles. They can be found in almost all major eukaryotic divisions, and genomic approaches are bringing major changes in our perception of their deep evolutionary relationships. At fine taxonomic levels, the generalization of barcoding is revealing a considerable and unsuspected specific diversity that can be appreciated with careful morphometric analyses based on light and electron microscopic observations. We provide examples on the difficulties and advances in amoeboid protists systematics in a selection of groups that were presented at the VIIIth ECOP/ISOP meeting in Rome, 2019. We conclude that, in all studied groups, important taxonomical rearrangements will certainly take place in the next few years, and systematics must be adapted to incorporate these changes. Notably, nomenclature should be flexible enough to integrate many new high level taxa, and a unified policy must be adopted to species description and to the establishment of types.

Paradoxical Survival: Examining the Parrondo Effect across Biology

Parrondo's paradox, in which losing strategies can be combined to produce winning outcomes, has received much attention in mathematics and the physical sciences; a plethora of exciting applications has also been found in biology at an astounding pace. In this review paper, the authors examine a large range of recent developments of Parrondo's paradox in biology, across ecology and evolution, genetics, social and behavioral systems, cellular processes, and disease. Intriguing connections between numerous works are identified and analyzed, culminating in an emergent pattern of nested recurrent mechanics that appear to span the entire biological gamut, from the smallest of spatial and temporal scales to the largest-from the subcellular to the complete biosphere. In analyzing the macro perspective, the pivotal role that the paradox plays in the shaping of biological life becomes apparent, and its identity as a potential universal principle underlying biological diversity and persistence is uncovered. Directions for future research are also discussed in light of this new perspective.

Lack of gene flow between Phytophthora infestans populations of two neighboring countries with the largest potato production

Gene flow is an important evolutionary force that enables adaptive responses of plant pathogens in response to changes in the environment and plant disease management strategies. In this study, we made a direct inference concerning gene flow in the Irish famine pathogen Phytophthora infestans between two of its hosts (potato and tomato) as well as between China and India. This was done by comparing sequence characteristics of the eukaryotic translation elongation factor 1 alpha (eEF-1α) gene, generated from 245 P. infestans isolates sampled from two countries and hosts. Consistent with previous results, we found that eEF-1α gene was highly conserved and point mutation was the only mechanism generating any sequence variation. Higher genetic variation was found in the eEF-1α sequences in the P. infestans populations sampled from tomato compared to those sampled from potato. We also found the P. infestans population from India displayed a higher genetic variation in the eEF-1α sequences compared to China. No gene flow was detected between the pathogen populations from the two countries, which is possibly attributed to the geographic barrier caused by Himalaya Plateau and the minimum cross-border trade of potato and tomato products. The implications of these results for a sustainable management of late blight diseases are discussed.

Systematic revision of the Tubifera casparyi-T. dictyoderma complex: Resurrection of the genus Siphoptychium and introduction of the new genus Thecotubifera

The genus Siphoptychium is resurrected on the basis of comparative morphology and phylogeny of partial nuc 18S rDNA (18S) and translation elongation factor 1-alpha (EF1A) nucleotide sequences. The genus is characterized by the firm upper surface of the pseudoaethalium, accreted but easily separable sporothecae, a tubular or fibrous columella, and spores with a reticulate ornamentation consisting of 7-9 meshes across the diameter. In addition to the currently known single species S. casparyi (= Tubifera casparyi), two new members of Siphoptychium are described: S. violaceum from coniferous forests of Europe, east Asia, and southeast Asia, and S. reticulatum from temperate and subarctic regions of North America and alpine regions of Europe. A second genus, Thecotubifera, is described to accommodate Tubifera dictyoderma. The fruiting body of this species is transitional between a pseudoaethalium and a true aethalium. It is covered by a contiguous membranous cortex formed by the fused tips of the sporothecae, a feature typical for aethalia. However, the inner portions of sporothecae remain discernible, a feature more typical for pseudoaethalia. Columellae of Th. dictyoderma are formed by perforated plates, and the spores have a reticulate ornamentation consisting of 2-5 meshes across the diameter. For Th. dictyoderma, we could confirm records only for tropical regions and Japan, whereas all studied European specimens, including those mentioned in current monographs, represent species of Siphoptychium.

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m⁷G-cap. The generation of the 3ʹ-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.

Interacting-heads motif has been conserved as a mechanism of myosin II inhibition since before the origin of animals

Electron microscope studies have shown that the switched-off state of myosin II in muscle involves intramolecular interaction between the two heads of myosin and between one head and the tail. The interaction, seen in both myosin filaments and isolated molecules, inhibits activity by blocking actin-binding and ATPase sites on myosin. This interacting-heads motif is highly conserved, occurring in invertebrates and vertebrates, in striated, smooth, and nonmuscle myosin IIs, and in myosins regulated by both Ca²⁺ binding and regulatory light-chain phosphorylation. Our goal was to determine how early this motif arose by studying the structure of inhibited myosin II molecules from primitive animals and from earlier, unicellular species that predate animals. Myosin II from Cnidaria (sea anemones, jellyfish), the most primitive animals with muscles, and Porifera (sponges), the most primitive of all animals (lacking muscle tissue) showed the same interacting-heads structure as myosins from higher animals, confirming the early origin of the motif. The social amoeba Dictyostelium discoideum showed a similar, but modified, version of the motif, while the amoeba Acanthamoeba castellanii and fission yeast (Schizosaccharomyces pombe) showed no head-head interaction, consistent with the different sequences and regulatory mechanisms of these myosins compared with animal myosin IIs. Our results suggest that head-head/head-tail interactions have been conserved, with slight modifications, as a mechanism for regulating myosin II activity from the emergence of the first animals and before. The early origins of these interactions highlight their importance in generating the inhibited (relaxed) state of myosin in muscle and nonmuscle cells.

Collective behaviour and swarm intelligence in slime moulds

The study of collective behaviour aims to understand how individual-level behaviours can lead to complex group-level patterns. Collective behaviour has primarily been studied in animal groups such as colonies of insects, flocks of birds and schools of fish. Although less studied, collective behaviour also occurs in microorganisms. Here, we argue that slime moulds are powerful model systems for solving several outstanding questions in collective behaviour. In particular, slime mould may hold the key to linking individual-level mechanisms to colony-level behaviours. Using well-established principles of collective animal behaviour as a framework, we discuss the extent to which slime mould collectives are comparable to animal groups, and we highlight some potentially fruitful areas for future research.

Identification of novel inhibitors of the translationally controlled tumor protein (TCTP): insights from molecular dynamics

The translationally controlled tumor protein (TCTP) is a highly conserved multifunctional protein, preferentially expressed in mitotically active tissues and is a potential biomarker and a therapeutic target for lung cancers. An understanding of the biology of this molecule and model systems for the screening of drugs is still awaited. In the absence of complete crystal structure, NMR structures as templates were used for homology modeling and MD optimization of both Dictyostelium discoideum and human TCTPs, which was followed by pocket-site prediction, ligand screening and docking. Rescoring of TCTP-ligand complexes was done using MD and MM-PBSA approaches. D. discoideum TCTP was expressed under a constitutive promoter and the endogenous RNA in multicellular structures formed was localized by in situ hybridization. Based on the interactions and binding energy scores, two novel compounds were identified as the best potential inhibitors that could be further used for the development of drug candidates. Inhibition of cell proliferation was observed in the strain overexpressing Dictyostelium TCTP and in situ hybridization results show them to be localized in the prestalk (dying cell population) cells. D. discoideum and human TCTPs share similar dynamic behaviors; overexpression of Dictyostelium TCTP inhibits cell proliferation. D. discoideum could be used as a model system for understanding the biology of this molecule and also for drug screening.

Evolution of Cell-Autonomous Effector Mechanisms in Macrophages versus Non-Immune Cells

Specialized adaptations for killing microbes are synonymous with phagocytic cells including macrophages, monocytes, inflammatory neutrophils, and eosinophils. Recent genome sequencing of extant species, however, reveals that analogous antimicrobial machineries exist in certain non-immune cells and also within species that ostensibly lack a well-defined immune system. Here we probe the evolutionary record for clues about the ancient and diverse phylogenetic origins of macrophage killing mechanisms and how some of their properties are shared with cells outside the traditional bounds of immunity in higher vertebrates such as mammals.

Speciation in progress? A phylogeographic study among populations of Hemitrichia serpula (Myxomycetes)

Myxomycetes (plasmodial slime molds, Amoebozoa) are often perceived as widely distributed, confounding to the “everything is everywhere” hypothesis. To test if gene flow within these spore-dispersed protists is restricted by geographical barriers, we chose the widespread but morphologically unmistakable species Hemitrichia serpula for a phylogeographic study. Partial sequences from nuclear ribosomal RNA genes (SSU) revealed 40 ribotypes among 135 specimens, belonging to three major clades. Each clade is dominated by specimens from a certain region and by one of two morphological varieties which can be differentiated by SEM micrographs. Partial sequences of the protein elongation factor 1 alpha (EF1A) showed each clade to possess a unique combination of SSU and EF1A genotypes. This pattern is best explained assuming the existence of several putative biospecies dominating in a particular geographical region. However, occasional mismatches between molecular data and morphological characters, but as well heterogeneous SSU and heterozygous EF1A sequences, point to ongoing speciation. Environmental niche models suggest that the putative biospecies are rather restricted by geographical barriers than by macroecological conditions. Like other protists, myxomycetes seem to follow the moderate endemicity hypothesis and are in active speciation, which is most likely shaped by limited gene flow and reproductive isolation.

Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression in Dictyostelium

Nucleosome placement and repositioning can direct transcription of individual genes; however, the precise interactions of these events are complex and largely unresolved at the whole-genome level. The Chromodomain-Helicase-DNA binding (CHD) Type III proteins are a subfamily of SWI2/SNF2 proteins that control nucleosome positioning and are associated with several complex human disorders, including CHARGE syndrome and autism. Type III CHDs are required for multicellular development of animals and Dictyostelium but are absent in plants and yeast. These CHDs can mediate nucleosome translocation in vitro, but their in vivo mechanism is unknown. Here, we use genome-wide analysis of nucleosome positioning and transcription profiling to investigate the in vivo relationship between nucleosome positioning and gene expression during development of wild-type (WT) Dictyostelium and mutant cells lacking ChdC, a Type III CHD protein ortholog. We demonstrate major nucleosome positional changes associated with developmental gene regulation in WT. Loss of chdC caused an increase of intragenic nucleosome spacing and misregulation of gene expression, affecting ∼50% of the genes that are repositioned during WT development. These analyses demonstrate active nucleosome repositioning during Dictyostelium multicellular development, establish an in vivo function of CHD Type III chromatin remodeling proteins in this process, and reveal the detailed relationship between nucleosome positioning and gene regulation, as cells transition between developmental states.

Mutations, evolution and the central role of a self-defined fitness function in the initiation and progression of cancer

The origin and progression of cancer is widely viewed as "somatic evolution" driven by the accumulation of random genetic changes. This theoretical model, however, neglects fundamental conditions for evolution by natural selection, which include competition for survival and a local environmental context. Recent observations that the mutational burden in different cancers can vary by 2 orders of magnitude and that multiple mutations, some of which are "oncogenic," are observed in normal tissue suggests these neglected Darwinian dynamics may play a critical role in modifying the evolutionary consequences of molecular events. Here we discuss evolutionary principles in normal tissue focusing on the dynamical tension between different evolutionary levels of selection. Normal somatic cells within metazoans do not ordinarily evolve because their survival and proliferation are governed by tissue signals and internal controls (e.g. telomere shortening) that maintain homeostatic function. The fitness of each cell is, thus, identical to the whole organism, which is the evolutionary level of selection. For a cell to evolve, it must acquire a self-defined fitness function so that its survival and proliferation is determined entirely by its own heritable phenotypic properties. Cells can develop independence from normal tissue control through randomly accumulating mutations that disrupt its ability to recognize or respond to all host signals. A self-defined fitness function can also be gained non-genetically when tissue control signals are lost due to injury, inflammation, or infection. Accumulating mutations in cells without a self-defined fitness function will produce no evolution - consistent with reports showing mutations, including some that would ordinarily be oncogenic, are present in cells from normal tissue. Furthermore, once evolution begins, Darwinian forces will promote mutations that increase fitness and eliminate those that do not. Thus, cancer cells will typically have a mutational burden similar to adjacent normal cells and many (perhaps most) mutations observed in cancer cells occurred prior to somatic evolution and may not contribute to the cell's malignant phenotype. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.

Nomadic-colonial life strategies enable paradoxical survival and growth despite habitat destruction

Organisms often exhibit behavioral or phenotypic diversity to improve population fitness in the face of environmental variability. When each behavior or phenotype is individually maladaptive, alternating between these losing strategies can counter-intuitively result in population persistence-an outcome similar to the Parrondo's paradox. Instead of the capital or history dependence that characterize traditional Parrondo games, most ecological models which exhibit such paradoxical behavior depend on the presence of exogenous environmental variation. Here we present a population model that exhibits Parrondo's paradox through capital and history-dependent dynamics. Two sub-populations comprise our model: nomads, who live independently without competition or cooperation, and colonists, who engage in competition, cooperation, and long-term habitat destruction. Nomads and colonists may alternate behaviors in response to changes in the colonial habitat. Even when nomadism and colonialism individually lead to extinction, switching between these strategies at the appropriate moments can paradoxically enable both population persistence and long-term growth.

Cellular differentiation and individuality in the 'minor' multicellular taxa

Biology needs a concept of individuality in order to distinguish organisms from parts of organisms and from groups of organisms, to count individuals and compare traits across taxa, and to distinguish growth from reproduction. Most of the proposed criteria for individuality were designed for 'unitary' or 'paradigm' organisms: contiguous, functionally and physiologically integrated, obligately sexually reproducing multicellular organisms with a germ line sequestered early in development. However, the vast majority of the diversity of life on Earth does not conform to all of these criteria. We consider the issue of individuality in the 'minor' multicellular taxa, which collectively span a large portion of the eukaryotic tree of life, reviewing their general features and focusing on a model species for each group. When the criteria designed for unitary organisms are applied to other groups, they often give conflicting answers or no answer at all to the question of whether or not a given unit is an individual. Complex life cycles, intimate bacterial symbioses, aggregative development, and strange genetic features complicate the picture. The great age of some of the groups considered shows that 'intermediate' forms, those with some but not all of the traits traditionally associated with individuality, cannot reasonably be considered ephemeral or assumed transitional. We discuss a handful of recent attempts to reconcile the many proposed criteria for individuality and to provide criteria that can be applied across all the domains of life. Finally, we argue that individuality should be defined without reference to any particular taxon and that understanding the emergence of new kinds of individuals requires recognizing individuality as a matter of degree.

Two-gene phylogeny of bright-spored Myxomycetes (slime moulds, superorder Lucisporidia)

Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ∼10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one Licea.

Switch-like reprogramming of gene expression after fusion of multinucleate plasmodial cells of two Physarum polycephalum sporulation mutants

Nonlinear dynamic processes involving the differential regulation of transcription factors are considered to impact the reprogramming of stem cells, germ cells, and somatic cells. Here, we fused two multinucleate plasmodial cells of Physarum polycephalum mutants defective in different sporulation control genes while being in different physiological states. The resulting heterokaryons established one of two significantly different expression patterns of marker genes while the plasmodial halves that were fused to each other synchronized spontaneously. Spontaneous synchronization suggests that switch-like control mechanisms spread over and finally control the entire plasmodium as a result of cytoplasmic mixing. Regulatory molecules due to the large volume of the vigorously streaming cytoplasm will define concentrations in acting on the population of nuclei and in the global setting of switches. Mixing of a large cytoplasmic volume is expected to damp stochasticity when individual nuclei deliver certain RNAs at low copy number into the cytoplasm. We conclude that spontaneous synchronization, the damping of molecular noise in gene expression by the large cytoplasmic volume, and the option to take multiple macroscopic samples from the same plasmodium provide unique options for studying the dynamics of cellular reprogramming at the single cell level.

Physarum polycephalum mutants in the photocontrol of sporulation display altered patterns in the correlated expression of developmentally regulated genes

Physarum polycephalum is a lower eukaryote belonging to the amoebozoa group of organisms that forms macroscopic, multinucleate plasmodial cells during its developmental cycle. Plasmodia can exit proliferative growth and differentiate by forming fruiting bodies containing mononucleate, haploid spores. This process, called sporulation, is controlled by starvation and visible light. To genetically dissect the regulatory control of the commitment to sporulation, we have isolated plasmodial mutants that are altered in the photocontrol of sporulation in a phenotypic screen of N-ethyl-N-nitrosourea (ENU) mutagenized cells. Several non-sporulating mutants were analyzed by measuring the light-induced change in the expression pattern of a set of 35 genes using GeXP multiplex reverse transcription-polymerase chain reaction with RNA isolated from individual plasmodial cells. Mutants showed altered patterns of differentially regulated genes in response to light stimulation. Some genes clearly displayed pairwise correlation in terms of their expression level as measured in individual plasmodial cells. The pattern of pairwise correlation differed in various mutants, suggesting that different upstream regulators were disabled in the different mutants. We propose that patterns of pairwise correlation in gene expression might be useful to infer the underlying gene regulatory network.

Physarum can compute shortest paths

Physarum polycephalum is a slime mold that is apparently able to solve shortest path problems. A mathematical model has been proposed by Tero et al. (Journal of Theoretical Biology, 244, 2007, pp. 553-564) to describe the feedback mechanism used by the slime mold to adapt its tubular channels while foraging two food sources s(0) and s(1). We prove that, under this model, the mass of the mold will eventually converge to the shortest s(0)-s(1) path of the network that the mold lies on, independently of the structure of the network or of the initial mass distribution. This matches the experimental observations by Tero et al. and can be seen as an example of a "natural algorithm", that is, an algorithm developed by evolution over millions of years.