Search Results (124)

The phenomenon of centromere clustering and its impact are still largely unclear in the eukaryotic supergroup of Amoebozoa. In this review, we highlight the molecular basis for centromere clustering, its relationship to the centrosome, and its role in mitotic spindle organization in Dictyostelium amoebae. Here, the centrosome is anchored to the cytosolic side of the nucleus during interphase and is connected via the nuclear envelope to the nuclear lamina and a cluster of the centromeres of all six chromosomes. Upon transition from the G2 phase to mitosis, the centrosome penetrates a fenestra in the persisting nuclear envelope and duplicates. During this process, microtubule connections are established between the mitotic centrosomes and the kinetochores. We review all known molecular players in this process and pose a hypothesis on how the centromere protein Cenp68, which is related to monopolin from fission yeast, could facilitate and accelerate the process of mitotic spindle formation. Full article

Copines are a family of calcium-dependent phospholipid-binding proteins conserved across numerous eukaryotes. The expression of multiple copine genes is dysregulated in several human cancers, yet their molecular functions remain poorly understood. We are investigating copine genes (cpnA-cpnF) in the amoeba Dictyostelium discoideum, a well-established model for studying conserved signaling pathways that regulate chemotaxis. During development, individual amoebae release and move toward cAMP. cAMP chemotaxis utilizes Ras/PI3K signaling, a pathway that is highly conserved in mammalian cells and often dysregulated in cancer. Using two cpnD mutants that were generated via restriction enzyme-mediated integration (REMI), we found that cpnD mutants exhibited increased cellular proliferation, precocious development, and larger fruiting bodies. Additionally, we found that cpnD mutants had increased cell spreading, producing a flattened morphology and larger cell area. Because activated Ras has been shown to promote this phenotype, we measured Ras activity and found that cpnD mutants exhibited increased Ras activation. cpnD mutants also formed significantly smaller contractile vacuoles during osmotic stress. Inhibition of PI3K suppressed both the enlarged cell area and reduced contractile vacuole phenotypes, indicating that these defects result from increased Ras/PI3K signaling. Finally, we found that GFP-tagged CpnD transiently localized to the plasma membrane following cAMP stimulation, suggesting CpnD may have a role in cAMP signaling. Together, these findings identify CpnD as a potential negative regulator of Ras signaling and provide the first evidence of copine involvement in the Ras/PI3K pathway, suggesting a conserved mechanism that may help explain how altered copine expression contributes to cancer progression. Full article

Mitochondrial dysfunction is increasingly recognized as a major contributor to central nervous system (CNS) disorders, including neurodegenerative and neuropsychiatric diseases. Animal models are essential for elucidating disease mechanisms and supporting the development of new therapeutic strategies. Among these models, non-mammalian organisms offer distinct advantages, including low cost, rapid life cycles, genetic tractability, and suitability for large-scale, high-throughput studies. Organisms such as Saccharomyces cerevisiae, Dictyostelium discoideum, Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio have substantially advanced the understanding of mitochondrial processes relevant to CNS pathology. Studies using these models have revealed conserved mechanisms involving mitophagy, mitochondrial quality control, respiratory function, bioenergetic signaling, and neurodegenerative pathways. Their strengths, including scalability, live imaging capacity, and efficient genetic manipulation, have accelerated disease modeling and therapeutic discovery. However, simplified physiology, evolutionary distance from humans, and the incomplete representation of complex CNS organization limit their translational relevance and often require validation in higher-order organisms. Nevertheless, integrating these models into CNS research, particularly alongside emerging technologies, provides a powerful strategy for linking fundamental mitochondrial biology with translational neuroscience. This review summarizes the use of non-mammalian models in neuroscience research, with an emphasis on mitochondrial dysfunction in CNS disorders and their potential to support future therapeutic advances. Full article

Based on their domain organisation, four proteins from the protist Dictyostelium discoideum have been assigned to the IQGAP family of scaffold proteins. Although these proteins are shorter than animal IQGAPs, their involvement in the regulation of the actin cytoskeleton in cell motility, macroendocytosis, cytokinesis, and adhesion appears to be broadly conserved between these evolutionarily distant organisms. In this article, we show that the putative three-dimensional structure of Dictyostelium IQGAP-related proteins, as predicted by AlphaFold 3, closely corresponds to the C-terminal half of human IQGAP1, thus supporting their common origin. IqgD is the largest IQGAP-related protein in Dictyostelium, with an overall domain organisation similar to human IQGAPs. IqgD is localised in the cell cortex, interacts with F-actin and Rac1 GTPases, and primarily supports cell adhesion to the underlying surface and cell growth on bacterial lawns. DGAP1 and GAPA are truncated proteins that have retained a 700-residue-long C-terminal region of homology compared to their animal relatives. They play important, yet opposite, roles in regulating contractile cortical assemblies comprising F-actin, myosin II, and the actin-bundling proteins cortexillins, which are especially important for cytokinesis and epithelial morphogenesis. Finally, IqgC, although structurally resembling other IQGAPs, turns out to be more closely related to GAP1 proteins from fungi. This multifaceted protein carries RasGAP activity, interacts with several other small GTPases, and positively regulates macroendocytosis and cell–substratum adhesion. Full article

Ether lipids in varying amounts are membrane constituents and storage material in the protist and animal kingdoms, but are largely absent from fungi and plants. Their biosynthesis pathway starts in the peroxisome and involves a set of well-conserved enzymes. Only one step, the reduction of alkyl-dihydroxyacetone-phosphate to alkyl-glycerol-3-phosphate, is mediated by so-called short-chain dehydrogenases/reductases, which are members of huge protein families. Here, using GFP fusions, we identify a peroxisomal enzyme in Dictyostelium, as well as a highly related protein residing in the endoplasmic reticulum. Single-gene knockouts indicate that these enzymes largely compensate for one another, suggesting a flexible redistribution of lipid metabolites between these organelles. The double knockout, however, is severely affected in ether lipid composition and displays a clear growth retardation. The defects can also be reverted by expression of the cognate yeast enzyme, demonstrating conservation of this metabolic step across kingdoms of life. Full article

Chemotaxis enables eukaryotic cells to detect and migrate along extracellular chemoattractant gradients spanning several orders of magnitude. This remarkable dynamic range relies on adaptation, a process that allows cells to reset their signaling machinery while preserving sensitivity to incremental changes in stimulus intensity. Although numerous actin-dependent feedback mechanisms have been characterized, the molecular basis of adaptation within an actin-independent core gradient-sensing module remains poorly understood. Here, we identify the Ras GTPase-activating protein, C2GAP1, as a critical F-actin-independent effector of the heterotrimeric G protein, Gα2, in Dictyostelium discoideum. Using cytoskeleton-free gradient-sensing cells, quantitative imaging, biochemical assays, FRET-based G-protein activation measurements, and structural modeling, we demonstrate that C2GAP1 controls concentration-dependent adaptation during gradient sensing. Mechanistically, C2GAP1 directly associates with Gα2 in both GDP- and GTP-bound states, with preferential binding to activated Gα2, thereby sustaining membrane recruitment and locally attenuating Ras and downstream signaling. Loss of C2GAP1 enhances G-protein activation, disrupts local inhibition, and impairs rapid reorientation in dynamic gradients. These findings define a direct coupling between heterotrimeric G proteins and the RasGAP, C2GAP1, as a core adaptive module that enables gradient sensing across a wide concentration range. Full article

Background: Dictyostelium discoideum is widely used in developmental and evolutionary biology due to its ability to transition from a single cell to a multicellular organism in response to starvation. While transcriptome information across its life cycle is widely available, only early-stage data exist at the proteome level. This study characterizes and compares the proteomes of D. discoideum cells at the vegetative, aggregation, mound, culmination and fruiting body stages. Methods: Samples were collected from cells developing synchronously on nitrocellulose filters. Proteins were extracted and digested with trypsin, and peptides were analyzed by liquid chromatography–tandem mass spectrometry. Data were processed using Proteome Discoverer™ for protein identification and label-free quantification. Results: A total of 4502 proteins were identified, of which 1848 (41%) were present across all stages. Pairwise comparisons between adjacent stages revealed clear transitions, the largest ones occurring between the culmination and fruiting body and between the fruiting body and vegetative stage, involving 29% and 52% of proteins, respectively. Hierarchical clustering assigned proteins to one of nine clusters, each displaying a distinct pattern of abundances across the life cycle. Conclusions: This study presents the first complete developmental proteomic time series for D. discoideum, revealing changes that contribute to multicellularity, cellular differentiation and morphogenesis. Full article

Chemorepulsion mechanisms for eukaryotic cells are poorly understood. We performed proteomics and phosphoproteomics to elucidate how Dictyostelium discoideum responds to its two endogenous chemorepellent signals, the protein AprA and inorganic polyphosphate (polyP). AprA and polyP affected levels of more than 200 proteins, with an overlap of both upregulating 25 proteins and downregulating two proteins. Two proteins were upregulated by AprA but downregulated by polyP, while two others showed the opposite trend. Surprisingly, many of the AprA- and polyP-regulated proteins are associated with RNA metabolism and ribosomes. AprA increased phosphorylation of 15 proteins and decreased phosphorylation of 36 proteins. PolyP increased phosphorylation of 12 proteins and decreased phosphorylation of 12 proteins. As expected, the two chemorepellents affected phosphorylation of signal transduction/ motility proteins, but unexpectedly affected phosphorylation of RNA-associated proteins. Both AprA and polyP decreased phosphorylation of five proteins including the Ras-interacting protein RipA and guanine nucleotide exchange factors (GEFs) such as the RacGEF GxcT. Mutants lacking RipA or GxcT were unresponsive to both AprA and polyP chemorepulsion. Together, this work supports the idea that rather than activating the same chemorepulsion mechanism, AprA and polyP activate only partially overlapping chemorepulsion mechanisms, and identifies two new components that are used by both chemorepellents. Full article

The social amoeba Dictyostelium discoideum is a versatile biological model widely used in drug discovery and studying cellular stress responses. However, its application for cytotoxicity evaluation of natural products, particularly algal-derived compounds, remains underutilized. In this study, we developed a high-throughput developmental assay in D. discoideum to analyze the cytotoxicity of acetone and methanol extracts from the Peruvian seaweed Glossophora kunthii. Our results showed that the acetone extract caused a transient delay in the social development of the amoeba. In contrast, the methanol extract exhibited no significant effects, even at high extract concentrations. UHPLC/Orbitrap/ESI/MS/MS analysis tentatively identified ten major compounds, including pachydictyol A and dictyotriol A diacetate. The presence of diterpenes, such as dictyotadiol and pachydictyol A, previously reported to exhibit moderate cytotoxic activity, likely explains the developmental delay observed with the acetone extract. This study highlights the utility of D. discoideum as a scalable cytotoxicity screening platform within algal pharmacognosy, facilitating the early identification of non-toxic marine natural products suitable for further biomedical and biotechnological development. Full article

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