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PLoS Computational Biology Aug 2021Navigation of fast migrating cells such as amoeba Dictyostelium and immune cells are tightly associated with their morphologies that range from steady polarized forms... (Comparative Study)
Comparative Study
Navigation of fast migrating cells such as amoeba Dictyostelium and immune cells are tightly associated with their morphologies that range from steady polarized forms that support high directionality to those more complex and variable when making frequent turns. Model simulations are essential for quantitative understanding of these features and their origins, however systematic comparisons with real data are underdeveloped. Here, by employing deep-learning-based feature extraction combined with phase-field modeling framework, we show that a low dimensional feature space for 2D migrating cell morphologies obtained from the shape stereotype of keratocytes, Dictyostelium and neutrophils can be fully mapped by an interlinked signaling network of cell-polarization and protrusion dynamics. Our analysis links the data-driven shape analysis to the underlying causalities by identifying key parameters critical for migratory morphologies both normal and aberrant under genetic and pharmacological perturbations. The results underscore the importance of deciphering self-organizing states and their interplay when characterizing morphological phenotypes.
Topics: Animals; Cell Movement; Cell Polarity; Cell Shape; Cell Surface Extensions; Cells, Cultured; Cichlids; Computational Biology; Computer Simulation; Deep Learning; Dictyostelium; Fibroblasts; HL-60 Cells; Humans; Models, Biological
PubMed: 34383753
DOI: 10.1371/journal.pcbi.1009237 -
Cell Biochemistry and Function Dec 2023Nutrient-sensing plays a crucial role in maintaining cellular energy and metabolic homeostasis. Perturbations in sensing pathways are associated with a wide variety of...
Nutrient-sensing plays a crucial role in maintaining cellular energy and metabolic homeostasis. Perturbations in sensing pathways are associated with a wide variety of pathologies, especially metabolic diseases. Very little is understood about sensing fluctuations in nutrients and how this information is integrated into physiological and metabolic adaptation that could further affect cell-fate decisions during differentiation in Dictyostelium discoideum (henceafter, Dictyostelium). Glucose is the primary metabolic fuel among all nutrients. Carbohydrates, lipids and proteins ultimately breakdown into glucose, which is further used for providing energy. The maintenance of optimum glucose levels is important for efficient cell-survival. Glucose is not only a nutrient, but also a signaling molecule influencing cell growth and differentiation in Dictyostelium. Modulation of endogenous glucose levels either by varying exogenous glucose levels or genetic overexpression or deletion of genes involved in glucose signaling lead to changes in endogenous metabolite levels such as ADP/ATP ratio, NAD /NADH ratio, cAMP and ROS levels which further influence cell-fate decisions. Here, we show that AMPKα and Sir2D are components of glucose-signaling pathway in Dictyostelium which adjust cell metabolism interdependently in response to nutrient-status and promote cell-fate decisions.
Topics: Dictyostelium; Signal Transduction; Cell Differentiation; Cell Cycle; Glucose
PubMed: 38014740
DOI: 10.1002/cbf.3892 -
Annual International Conference of the... Nov 2021Although spatiotemporal changes of oxygen in a microenvironment are known to affect the cellular dynamics of various eukaryotes, the details are not fully understood....
Although spatiotemporal changes of oxygen in a microenvironment are known to affect the cellular dynamics of various eukaryotes, the details are not fully understood. Here, we describe the aerotaxis and aerokinesis of Dictyostelium discoideum (Dd), which has long been employed as a model organism for eukaryotic cells. We developed a microfluidic device capable of time-lapse observation of cultured cells while controlling oxygen concentrations in microchannels. Migratory behaviors of Dd were observed and quantitatively evaluated under an oxygen concentration gradient from 0% to 21% O, as well as in various uniform oxygen conditions. In a hypoxic region within the oxygen concentration gradient, Dd migrated toward regions of higher oxygen concentration at increased velocity, which was independent of cell density. Observed under uniform oxygen concentrations of 1%, 2%, 3%, and 21%, the migration velocity of Dd increased significantly in hypoxic environments of 2% O or less. Thus, Dd shows aerotaxis, directed by the oxygen concentration gradient, and simultaneously shows aerokinesis, changing the migration velocity according to the oxygen concentration itself.
Topics: Cell Line; Cells, Cultured; Chemotaxis; Dictyostelium; Oxygen
PubMed: 34891499
DOI: 10.1109/EMBC46164.2021.9629752 -
FEBS Open Bio Jun 2020Copines are a family of cytosolic proteins that associate with membranes in a calcium-dependent manner and are found in many eukaryotic organisms....
Copines are a family of cytosolic proteins that associate with membranes in a calcium-dependent manner and are found in many eukaryotic organisms. Dictyostelium discoideum has six copine genes (cpnA-cpnF), and cells lacking cpnA(cpnA ) have defects in cytokinesis, chemotaxis, adhesion, and development. CpnA has also been shown to associate with the plasma membrane, contractile vacuoles (CV), and organelles of the endolysosomal pathway. Here, we use cpnA cells to investigate the role of CpnA in CV function and endocytosis. When placed in water, cpnA cells made abnormally large CVs that took longer to expel. Visualization of CVs with the marker protein GFP-dajumin indicated that cpnA cells had fewer CVs that sometimes refilled before complete emptying. In endocytosis assays, cpnA cells took up small fluorescent beads by macropinocytosis at rates similar to parental cells. However, cpnA cells reached a plateau sooner than parental cells and had less fluorescence at later time points. p80 antibody labeling of postlysosomes (PL) indicated that there were fewer and smaller PLs in cpnA cells. In dextran pulse-chase experiments, the number of PLs peaked earlier in cpnA cells, and the PLs did not become as large and disappeared sooner as compared to parental cells. PLs in cpnA cells were also shown to have more actin coats, suggesting CpnA may play a role in actin filament disassembly on PL membranes. Overall, these results indicate that CpnA is involved in the regulation of CV size and expulsion, and the maturation, size, and exocytosis of PLs.
Topics: Carrier Proteins; Cell Line; Cell Membrane; Chemotaxis; Dictyostelium; Exocytosis; Gene Knockout Techniques; Genes, Reporter; Green Fluorescent Proteins; Intravital Microscopy; Microscopy, Fluorescence; Protozoan Proteins; Time-Lapse Imaging; Vacuoles
PubMed: 32351039
DOI: 10.1002/2211-5463.12874 -
Frontiers in Cell and Developmental... 2023Amoeboid cell movement and migration are wide-spread across various cell types and species. Microscopy-based analysis of the model systems and neutrophils over the...
Amoeboid cell movement and migration are wide-spread across various cell types and species. Microscopy-based analysis of the model systems and neutrophils over the years have uncovered generality in their overall cell movement pattern. Under no directional cues, the centroid movement can be quantitatively characterized by their persistence to move in a straight line and the frequency of re-orientation. Mathematically, the cells essentially behave as a persistent random walker with memory of two characteristic time-scale. Such quantitative characterization is important from a cellular-level ethology point of view as it has direct connotation to their exploratory and foraging strategies. Interestingly, outside the amoebozoa and metazoa, there are largely uncharacterized species in the excavate taxon Heterolobosea including amoeboflagellate . While classical works have shown that these cells indeed show typical amoeboid locomotion on an attached surface, their quantitative features are so far unexplored. Here, we analyzed the cell movement of by employing long-time phase contrast imaging that automatically tracks individual cells. We show that the cells move as a persistent random walker with two time-scales that are close to those known in and neutrophils. Similarities were also found in the shape dynamics which are characterized by the appearance, splitting and annihilation of the curvature waves along the cell edge. Our analysis based on the Fourier descriptor and a neural network classifier point to importance of morphology features unique to including complex protrusions and the transient bipolar dumbbell morphologies.
PubMed: 38020930
DOI: 10.3389/fcell.2023.1274127 -
Cytoskeleton (Hoboken, N.J.) Aug 2020Actin waves are F-actin-rich entities traveling on the ventral plasma membrane by the treadmilling mechanism. Actin waves were first discovered and are best...
Actin waves are F-actin-rich entities traveling on the ventral plasma membrane by the treadmilling mechanism. Actin waves were first discovered and are best characterized in Dictyostelium. Class I myosins are unconventional monomeric myosins that bind lipids through their tails. Dictyostelium has seven class I myosins, six of these have tails (Myo1A-F) while one has a very short tail (Myo1K), and three of them (Myo1D, Myo1E and Myo1F) bind PIP3 with high affinity. Localization of five Dictyostelium Class I myosins synchronizes with localization and propagation of actin waves. Myo1B and Myo1C colocalize with actin in actin waves, whereas Myo1D, E and F localize to the PIP3-rich region surrounded by actin waves. Here, we studied the effect of overexpression of the three PIP3 specific Class I myosins on actin waves. We found that ectopic expression of the short-tail Myo1F inhibits wave formation, short-tail Myo1E has similar but weaker inhibitory effect, but long-tail Myo1D does not affect waves. A study of Myo1F mutants shows that its membrane-binding site is absolutely required for wave inhibition, but the head portion is not. The results suggest that PIP3 specificity and the presence of two membrane-binding sites are required for inhibition of actin waves, and that inhibition may be caused by crosslinking of PIP3 heads groups.
Topics: Actin Cytoskeleton; Dictyostelium; Myosins
PubMed: 32734648
DOI: 10.1002/cm.21627 -
PloS One 2021Amoeboid cells constantly change shape and extend protrusions. The direction of movement is not random, but is correlated with the direction of movement in the preceding...
Amoeboid cells constantly change shape and extend protrusions. The direction of movement is not random, but is correlated with the direction of movement in the preceding minutes. The basis of this correlation is an underlying memory of direction. The presence of memory in movement is known for many decades, but its molecular mechanism is still largely unknown. This study reports in detail on the information content of directional memory, the kinetics of learning and forgetting this information, and the molecular basis for memory using Dictyostelium mutants. Two types of memory were characterized. A short-term memory stores for ~20 seconds the position of the last pseudopod using a local modification of the branched F-actin inducer SCAR/WAVE, which enhances one new pseudopod to be formed at the position of the previous pseudopod. A long term memory stores for ~2 minutes the activity of the last ~10 pseudopods using a cGMP-binding protein that induces myosin filaments in the rear of the cell; this inhibits pseudopods in the rear and thereby enhances pseudopods in the global front. Similar types of memory were identified in human neutrophils and mesenchymal stem cells, the protist Dictyostelium and the fungus B.d. chytrid. The synergy of short- and long-term memory explains their role in persistent movement for enhanced cell dispersal, food seeking and chemotaxis.
Topics: Cell Movement; Cell Polarity; Dictyostelium; Memory, Long-Term; Memory, Short-Term; Mutation; Pseudopodia
PubMed: 33571271
DOI: 10.1371/journal.pone.0246345 -
Nature Mar 2021The behaviour of Dictyostelium discoideum depends on nutrients. When sufficient food is present these amoebae exist in a unicellular state, but upon starvation they...
The behaviour of Dictyostelium discoideum depends on nutrients. When sufficient food is present these amoebae exist in a unicellular state, but upon starvation they aggregate into a multicellular organism. This biology makes D. discoideum an ideal model for investigating how fundamental metabolism commands cell differentiation and function. Here we show that reactive oxygen species-generated as a consequence of nutrient limitation-lead to the sequestration of cysteine in the antioxidant glutathione. This sequestration limits the use of the sulfur atom of cysteine in processes that contribute to mitochondrial metabolism and cellular proliferation, such as protein translation and the activity of enzymes that contain an iron-sulfur cluster. The regulated sequestration of sulfur maintains D. discoideum in a nonproliferating state that paves the way for multicellular development. This mechanism of signalling through reactive oxygen species highlights oxygen and sulfur as simple signalling molecules that dictate cell fate in an early eukaryote, with implications for responses to nutrient fluctuations in multicellular eukaryotes.
Topics: Amino Acids, Essential; Antioxidants; Cell Aggregation; Cell Differentiation; Cell Proliferation; Cell Respiration; Cysteine; Dictyostelium; Food Deprivation; Glutathione; Iron-Sulfur Proteins; Mitochondria; Nutrients; Oxygen; Reactive Oxygen Species; Signal Transduction; Sulfur
PubMed: 33627869
DOI: 10.1038/s41586-021-03270-3 -
Cellular Signalling Jun 2020The neuronal ceroid lipofuscinoses (NCLs) are a family of neurodegenerative diseases that affect people of all ages and ethnicities, yet many of the associated...
The neuronal ceroid lipofuscinoses (NCLs) are a family of neurodegenerative diseases that affect people of all ages and ethnicities, yet many of the associated genes/proteins are not well characterized. Mutations in MFSD8 (major facilitator superfamily domain-containing 8) cause an infantile form of NCL referred to as CLN7 disease. In this study, we revealed the localization and binding partners of an ortholog of human MFSD8 (Mfsd8) in the social amoeba Dictyostelium discoideum. Putative lysosomal targeting motifs are conserved in Dictyostelium Mfsd8, as are several residues mutated in CLN7 disease patients. Mfsd8 tagged with GFP localizes to endocytic compartments, which includes acidic intracellular vesicles and late endosomes. We pulled-down GFP-Mfsd8 and used mass spectrometry to reveal the Mfsd8 interactome during Dictyostelium growth and starvation. Among the identified hits were the Dictyostelium ortholog of human cathepsin D (CtsD), as well as proteins linked to the functions of the CLN3 (Cln3) and CLN5 (Cln5) orthologs in Dictyostelium. To study the function of Mfsd8, we validated a publically available mfsd8 cell line (GWDI Project) and then used this knockout cell line to show that Mfsd8 influences the secretion of Cln5 and CtsD. This information is then integrated into an emerging model describing the molecular networking of NCL proteins in Dictyostelium. In total, this study identifies Dictyostelium as a new model system for studying CLN7 disease.
Topics: Cathepsin D; Dictyostelium; Humans; Lysosomal Membrane Proteins; Membrane Transport Proteins; Mutation; Neuronal Ceroid-Lipofuscinoses; Protozoan Proteins
PubMed: 32087303
DOI: 10.1016/j.cellsig.2020.109572 -
Cells Jun 2020Multinucleate cells can be produced in by electric pulse-induced fusion. In these cells, unilateral cleavage furrows are formed at spaces between areas that are...
Multinucleate cells can be produced in by electric pulse-induced fusion. In these cells, unilateral cleavage furrows are formed at spaces between areas that are controlled by aster microtubules. A peculiarity of unilateral cleavage furrows is their propensity to join laterally with other furrows into rings to form constrictions. This means cytokinesis is biphasic in multinucleate cells, the final abscission of daughter cells being independent of the initial direction of furrow progression. Myosin-II and the actin filament cross-linking protein cortexillin accumulate in unilateral furrows, as they do in the normal cleavage furrows of mononucleate cells. In a myosin-II-null background, multinucleate or mononucleate cells were produced by cultivation either in suspension or on an adhesive substrate. Myosin-II is not essential for cytokinesis either in mononucleate or in multinucleate cells but stabilizes and confines the position of the cleavage furrows. In fused wild-type cells, unilateral furrows ingress with an average velocity of 1.7 µm × min, with no appreciable decrease of velocity in the course of ingression. In multinucleate myosin-II-null cells, some of the furrows stop growing, thus leaving space for the extensive broadening of the few remaining furrows.
Topics: Cell Division; Cell Fusion; Cell Membrane; Cytokinesis; Dictyostelium; Gene Knockout Techniques; Genes, Protozoan; Green Fluorescent Proteins; Microfilament Proteins; Myosin Type II; Protozoan Proteins; Recombinant Fusion Proteins
PubMed: 32570994
DOI: 10.3390/cells9061493