Search Results (114)

The bioproduction of high-value molecules offers a sustainable and cost-effective alternative to traditional extraction and chemical synthesis, particularly for complex metabolites like cannabinoids (CBs), which have therapeutic potential for neurodegenerative diseases. The marine diatom Phaeodactylum tricornutum presents a promising chassis for CB biosynthesis due to its high lipid content, essential building blocks to biosynthesize CBs. In this study, we explored the feasibility of producing olivetolic acid (OA), the key CB precursor, using a hybrid-type polyketide synthase, SteelyA, from Dictyostelium discoideum. Unlike the native Cannabis sativa enzymes—tetraketide synthase and olivetolic acid cyclase—which exhibit low productivity and stability in diatoms, SteelyA was expected to offer an alternative biosynthetic route. Heterologous production in P. tricornutum resulted in a C-terminal fragment of the SteelyA enzyme, suggesting partial expression or processing of the very high-molecular-weight (352 kDa) SteelyA protein over six months without affecting cellular growth. However, HPLC-MS analysis did not detect intracellular OA or its derivatives in vivo and in vitro, suggesting enzymatic inactivity or metabolic limitations. These negative findings highlight the need for further investigation into the metabolic and proteomic requirements for CB precursor biosynthesis in diatoms, guiding future optimization strategies for sustainable cannabinoid production. Full article

The cellular slime mould Dictyostelium discoideum is a soil-dwelling eukaryotic organism that undergoes distinctive morphological changes during starvation, making it a promising candidate for bioassay development. In this study, we evaluated the effects of copper (Cu) exposure on the morphological transformation of D. discoideum and performed a comparative proteomic analysis. Copper exposure on agar media delayed aggregate formation by 3.5 h compared to the controls. Approximately 280 protein spots were detected using immobilised pH gradient two-dimensional gel electrophoresis followed by silver staining. Three spots disappeared upon exposure to Cu. Based on isoelectric point and molecular weight analyses, the proteins were predicted to be formin-1, a cytoplasmic regulator of adenylyl cyclase (CRAC), and a tetratricopeptide repeat (TPR)-containing protein. Formin-1 and CRAC are involved in aggregation processes. These findings suggest that Cu disrupts aggregation-related protein expression in D. discoideum and highlight the potential of D. discoideum-based bioassays using proteomic biomarkers for environmental monitoring. Full article

Dictyostelium discoideum (Dicty) is a type of unicellular amoeba, but when starved, a large number of amoebas gather together to form a multicellular organism. In this review, we first introduce our cellular dynamics method for Dicty, including intracellular biochemical reactions. We then introduce a number of hidden roles of receptors revealed by our simulation studies. Of particular note is that receptor–receptor interactions are strengthened under starvation conditions, resulting in diverse dynamic functions that cannot be predicted from the action of a single receptor, such as intercellular synchronization. Furthermore, we introduce a mathematical generalization of Dicty’s receptor function and demonstrate its potential applications not only in the biological field but also in the engineering field. Full article

Background/Objectives: Codon usage bias affects gene expression and translation efficiency across species. The effective number of codons (ENC) and GC content influence codon preference, often displaying unimodal or bimodal distributions. This study investigates the correlation between ENC and GC rankings across species and how their relationship affects codon usage distributions. Methods: I analyzed nuclear-encoded genes from 17 species representing six kingdoms: one bacteria (Escherichia coli), three fungi (Saccharomyces cerevisiae, Neurospora crassa, and Schizosaccharomyces pombe), one archaea (Methanococcus aeolicus), three protists (Rickettsia hoogstraalii, Dictyostelium discoideum, and Plasmodium falciparum),), three plants (Musa acuminata, Oryza sativa, and Arabidopsis thaliana), and six animals (Anopheles gambiae, Apis mellifera, Polistes canadensis, Mus musculus, Homo sapiens, and Takifugu rubripes). Genes in all 17 species were ranked by GC content and ENC, and correlations were assessed. I examined how adding or subtracting these rankings influenced their overall distribution in a new method that I call Two-Rank Order Normalization or TRON. The equation, TRON = SUM(ABS((GC rank₁:GC rank_N) − (ENC rank₁:ENC rank_N))/(N²/3), where (GC rank₁:GC rank_N) is a rank-order series of GC rank, (ENC rank₁:ENC rank_N) is a rank-order series ENC rank, sorted by the rank-order series GC rank. The denominator of TRON, N²/3, is the normalization factor because it is the expected value of the sum of the absolute value of GC rank–ENC rank for all genes if GC rank and ENC rank are not correlated. Results: ENC and GC rankings are positively correlated (i.e., ENC increases as GC increases) in AT-rich species such as honeybees (R² = 0.60, slope = 0.78) and wasps (R² = 0.52, slope = 0.72) and negatively correlated (i.e., ENC decreases as GC increases) in GC-rich species such as humans (R² = 0.38, slope = −0.61) and rice (R² = 0.59, slope = −0.77). Second, the GC rank–ENC rank distributions change from unimodal to bimodal as GC content increases in the 17 species. Third, the GC rank+ENC rank distributions change from bimodal to unimodal as GC content increases in the 17 species. Fourth, the slopes of the correlations (GC versus ENC) in all 17 species are negatively correlated with TRON (R² = 0.98) (see Graphic Abstract). Conclusions: The correlation between ENC rank and GC rank differs among species, shaping codon usage distributions in opposite ways depending on whether a species’ nuclear-encoded genes are AT-rich or GC-rich. Understanding these patterns might provide insights into translation efficiency, epigenetics mediated by CpG DNA methylation, epitranscriptomics of RNA modifications, RNA secondary structures, evolutionary pressures, and potential applications in genetic engineering and biotechnology. Full article

Dictyostelium is a unique model used to study the complex and interactive cyclic nucleotide signaling pathways that regulate multicellular development. Dictyostelium grow as individual single cells, but in the absence of nutrients, they initiate a multicellular developmental program. Central to this is secreted cAMP, a primary GPCR-response signal. Activated cAMP receptors at the cell surface direct a number of downstream signaling pathways, including synthesis of the intracellular second messengers cAMP and cGMP. These, in turn, activate a series of downstream targets that direct chemotaxis within extracellular cAMP gradients, multicellular aggregation, and, ultimately, cell-specific gene expression, morphogenesis, and cytodifferentiation. Extracellular cAMP and intracellular cAMP and cGMP exhibit rapid fluctuations in concentrations and are, thus, subject to exquisite regulation by both synthesis and degradation. The Dictyostelium genome encodes seven phosphodiesterases (PDEs) that degrade cyclic nucleotides to nucleotide 5’-monophosphates. Each PDE has a distinct structure, substrate specificity, regulatory input, cellular localization, and developmentally regulated expression pattern. The intra- or extra-cellular localizations and enzymatic specificities for cAMP or cGMP are essential for degradative precision at different developmental stages. We discuss the diverse PDEs, the nucleotide cyclases, and the target proteins for cAMP and cGMP in Dictyostelium. We further outline the major molecular, cellular, and developmental events regulated by cyclic nucleotide signaling, with emphasis on the input of each PDE and consequence of loss-of-function mutations. Finally, we relate the structures and functions of the Dictyostelium PDEs with those of humans and in the context of potential therapeutic understandings. Full article

Moringa oleifera Lam (MO) is a member of the Moringaceae family and has been widely used as a traditional form of treatment for various diseases due to its high nutrient content. The plant is rich in vitamins, minerals, organic acids, phenolic compounds, polyphenols, alkaloids, and flavonoids. However, the concentrations of these components in each part of the plant differ, leading to specific beneficial uses. In this study, we aimed to analyze the contents of Moringa oleifera leaf (ML) and Moringa oleifera root (MR) extracts and characterize the effects of these extracts on cell behavior. HPLC analysis data showed a higher level of flavonoids and apigenin in the ML extract compared to the MR extract. Furthermore, CG/MS analysis revealed 54 components in the ML extract, with only 3 (ethyl palmitate, ethyl linolenate, and palmitic acid, 2-(octadecyloxy)ethyl ester) of them being at high levels. In this study, Dictyostelium discoideum was used as a cellular model and D. discoideum’s cell growth, chemotaxis, and development life cycle were investigated. The data presented herein demonstrate a significant decrease in cell growth and that the completion of the development life cycle was delayed in the ML extract-treated sample. This effect was not found in the untreated cells and MR extract-treated samples. In addition, the ability of cells to stream during chemotaxis was not inhibited following treatments. These findings suggested that ML extract has an impact on cell proliferation and cell directed migration processes, where the high level of flavonoids and apigenin in this extract can be a strong factor that led to these results. Full article

In the last decades, the study of many nuclear envelope components in Dictyostelium amoebae has revealed conserved mechanisms of nuclear envelope dynamics that root back unexpectedly deep into the eukaryotic tree of life. In this review, we describe the state of the art in nuclear envelope research in this organism starting from early work on nuclear pore complexes to characterization of the first true lamin in a non-metazoan organism and its associated nuclear envelope transmembrane proteins, such as the HeH-family protein Src1 and the LINC complex protein Sun1. We also describe the dynamic processes during semi-closed mitosis, including centrosome insertion into the nuclear envelope, and processes involved in the restoration of nuclear envelope permeability around mitotic exit and compare them to the situation in cells with open or fully closed mitosis. Full article

ADP-ribosylation is a reversible modification of proteins and nucleic acids, which controls major cellular processes, including DNA damage repair, cell proliferation and differentiation, metabolism, stress, and immunity in plants and animals. The involvement of ADP-ribosylation in the life cycle of Dictyostelium and some filamentous fungi has also been demonstrated. However, the role of this process in pathogenic oomycetes has never been addressed. Here, we show that the Phytophthora infestans genome contains two PARP-like protein genes (PiPARP1 and PiPARP2), and provide evidence of PARylation activity for one of them (PiPARP2). Using dsRNA-mediated RNA silencing of the PiPARP2 gene and chemical (pharmacological) inhibition of PARP activity by 3-aminobenzamide (3AB) PARP inhibitor, we demonstrate the critical functional role of ADP-ribosylation in Phytophthora mycelium growth. Virulence test on detached leaves also suggests an important role of ADP-ribosylation in Phytophthora host plant colonisation and pathogenesis. On a practical level, our data suggest that targeting the PARylation system may constitute a novel powerful approach for the management of Phytophthora diseases. Full article

Dictyostelids represent a crucial element in the protist community, and their abundant presence in Jilin Province underscores their indispensable role in biodiversity conservation. In the present study, a resource survey of dictyostelids used random sampling to collect 28 soil samples from five localities in Changbai Korean Autonomous County, Jilin Province. In addition, a compilation of dictyostelid species reported from Jilin Province was developed, based on a thorough review of the literature. The survey yielded fifteen isolates of dictyostelids, comprising six species from four genera. Notably, two new species (Dictyostelium longigracilis sp. nov. and Dictyostelium macrosoriobrevipes sp. nov.) were described using morphological characteristics and SSU gene-based phylogenetic analyses. One other species (Polysphondylium patagonicum) was recorded as new for China, while another (Cavenderia aureostipes) was recorded as a new record for Jilin Province. The dictyostelid assemblage in Jilin Province is dominated by the genus Dictyostelium (51.4%), with a total of 35 species, which represent 59.3% of the current total known for all of China. These findings provide a scientific basis for the protection of species diversity and resource utilization of dictyostelids in Jilin Province. Full article

Shear stress plays a crucial role in modulating cell adhesion and signaling. We present a microfluidic shear stress generator used to investigate the adhesion dynamics of Dictyostelium discoideum, an amoeba cell model organism with well-characterized adhesion properties. We applied shear stress and tracked cell adhesion, motility, and detachment using time-lapse videomicroscopy. In the precise shear conditions generated on-chip, our results show cell migration patterns are influenced by shear stress, with cells displaying an adaptive response to shear forces as they alter their adhesion and motility behavior. Additionally, we observed that DH1-10 wild-type D. discoideum cells exhibit stronger adhesion and resistance to shear-induced detachment compared to phg2 adhesion-defective mutant cells. We also highlight the influence of cell density on detachment kinetics. Full article

Morchella spp. (true morels) are precious edible mushrooms consumed around the world, with a delicious taste, rich nutritional value, and unique healthcare effects. Various fungi and bacteria have been reported to colonize the ascocarps of Morchella, damaging their fruiting bodies and leading to serious economic losses in cultivation. The species identification of these colonizing organisms is crucial for understanding their colonization mechanisms on morels. Slime molds, which have characteristics of both “fungi” and “animals”, can occasionally colonize crops and edible fungi. However, there have been no reports of dictyostelid cellular slime molds (dictyostelids) colonizing plants and fungi to date. In this study, we discovered that dictyostelids colonized the surface of one wild ascoma of Morchella in the forest of Chongqing, China, with the tissues being black and rotten. Macro- and micro-morphological observations, along with molecular phylogenetic analyses, identified the specimens investigated in this study as Dictyostelium implicatum and Morchella sp. Mel-21. The results provide new knowledge of dictyostelid colonization on organisms and contribute to the diversity of species colonizing true morels. Moreover, this is also the first report of dictyostelids distributed in Chongqing, China. This study enhances our insights into the life history and potential ecological significance of dictyostelids and updates their distribution area in China. Further research will be conducted to uncover the mechanisms behind the colonization observed in this study. Full article

Francisella is a highly infectious gram-negative bacterium that causes tularemia in humans and animals. It can survive and multiply in a variety of cells, including macrophages, dendritic cells, amoebae, and arthropod-derived cells. However, the intracellular life cycle of a bacterium varies depending on the cell type. Shortly after the infection of mammalian cells, the bacterium escapes the phagosome into the cytosol, where it replicates. In contrast, in the amoebae Acanthamoeba castellanii and Hartmannella vermiformis, the bacterium replicates within the membrane-bound vacuole. In recent years, the amoeba Dictyostelium discoideum has emerged as a powerful model to study the intracellular cycle and virulence of many pathogenic bacteria. In this study, we used D. discoideum as a model for the infection and isolation of Francisella novicida-containing vacuoles (FCVs) formed after bacteria invade the amoeba. Our results showed that F. novicida localized in a vacuole after invading D. discoideum. Here, we developed a method to isolate FCV and determined its composition by proteomic analyses. Proteomic analyses revealed 689 proteins, including 13 small GTPases of the Rab family. This is the first evidence of F. novicida-containing vacuoles within amoeba, and this approach will contribute to our understanding of host–pathogen interactions and the process of pathogen vacuole formation, as vacuoles containing bacteria represent direct contact between pathogens and their hosts. Furthermore, this method can be translocated on other amoeba models. Full article

The centrosome of the amoebozoan model Dictyostelium discoideum provides the best-established model for an acentriolar centrosome outside the Opisthokonta. Dictyostelium exhibits an unusual centrosome cycle, in which duplication is initiated only at the G2/M transition and occurs entirely during the M phase. Little is known about the role of conserved centrosomal kinases in this process. Therefore, we have generated knock-in strains for Aurora (AurK), CDK1, cyclin B, Nek2, and Plk, replacing the endogenous genes with constructs expressing the respective green fluorescent Neon fusion proteins, driven by the endogenous promoters, and studied their behavior in living cells. Our results show that CDK1 and cyclin B arrive at the centrosome first, already during G2, followed by Plk, Nek2, and AurK. Furthermore, CDK1/cyclin B and AurK were dynamically localized at kinetochores, and AurK in addition at nucleoli. The putative roles of all four kinases in centrosome duplication, mitosis, cytokinesis, and nucleolar dynamics are discussed. Full article

Autophagy is a degradative recycling process central to the maintenance of homeostasis in all eukaryotes. By ensuring the degradation of damaged mitochondria, it plays a key role in maintaining mitochondrial health and function. Of the highly conserved autophagy proteins, autophagy-related protein 1 (Atg1) is essential to the process. The involvement of these proteins in intracellular signalling pathways, including those involving mitochondrial function, are still being elucidated. Here the role of Atg1 was investigated in the simple model organism Dictyostelium discoideum using an atg1 null mutant and mutants overexpressing or antisense-inhibiting atg1. When evaluated against the well-characterised outcomes of mitochondrial dysfunction in this model, altered atg1 expression resulted in an unconventional set of phenotypic outcomes in growth, endocytosis, multicellular development, and mitochondrial homeostasis. The findings here show that Atg1 is involved in a tightly regulated signal transduction pathway coordinating energy-consuming processes such as cell growth and multicellular development, along with nutrient status and energy production. Furthermore, Atg1’s effects on energy homeostasis indicate a peripheral ancillary role in the mitochondrial signalling network, with effects on energy balance rather than direct effects on electron transport chain function. Further research is required to tease out these complex networks. Nevertheless, this study adds further evidence to the theory that autophagy and mitochondrial signalling are not opposing but rather linked, yet strictly controlled, homeostatic mechanisms. Full article

Cell-to-cell communication is fundamental to the organization and functionality of multicellular organisms. Intercellular signals orchestrate a variety of cellular responses, including gene expression and protein function changes, and contribute to the integrated functions of individual tissues. Dictyostelium discoideum is a model organism for cell-to-cell interactions mediated by chemical signals and multicellular formation mechanisms. Upon starvation, D. discoideum cells exhibit coordinated cell aggregation via cyclic adenosine 3′,5′-monophosphate (cAMP) gradients and chemotaxis, which facilitates the unicellular-to-multicellular transition. During this process, the calcium signaling synchronizes with the cAMP signaling. The resulting multicellular body exhibits organized collective migration and ultimately forms a fruiting body. Various signaling molecules, such as ion signals, regulate the spatiotemporal differentiation patterns within multicellular bodies. Understanding cell-to-cell and ion signaling in Dictyostelium provides insight into general multicellular formation and differentiation processes. Exploring cell-to-cell and ion signaling enhances our understanding of the fundamental biological processes related to cell communication, coordination, and differentiation, with wide-ranging implications for developmental biology, evolutionary biology, biomedical research, and synthetic biology. In this review, I discuss the role of ion signaling in cell motility and development in D. discoideum. Full article