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The International Journal of... 2019Multi-protein complexes mTORC1 and mTORC2 are required for growth and development of eukaryotes. mTORC1 is a nutrient sensor that integrates metabolic signals and energy... (Review)
Review
Multi-protein complexes mTORC1 and mTORC2 are required for growth and development of eukaryotes. mTORC1 is a nutrient sensor that integrates metabolic signals and energy state to regulate cell growth/proliferation, whereas, mTORC2 primarily regulates developmental processes. Dictyostelium proliferate in rich growth media, but initiate development upon nutrient depletion. Both mTOR complexes play essential roles in Dictyostelium, where growth and developmental cycles independently require, respectively, mTORC1 or mTORC2. Many protein associations and regulatory pathways for mTORC1 and mTORC2 in Dictyostelium have context similarity to mammalian cells and specificity to inhibition by the immunosuppressive drug rapamycin. In Dictyostelium, mTORC1 function is inactivated upon starvation-induced development, but development is directly induced through rapamycin-mediated inhibition of mTORC1 activity, even in the absence of nutrient withdrawal. Pharmacologic inhibition of mTORC1, in the absence of nutrient loss, has allowed the identification of a class of essential up-regulated, developmentally-associated signaling genes and down-regulated, growth genes. We also review functional pathway regulations that integrate mTORC1/mTORC2 activities and emphasize complexity of small GTPase regulation of mTORC2 activity. Finally, epistases experiments have suggested novel upstream pathway cross-talk in Dictyostelium that requires mTORC1 and mTORC2, but for separate and independent downstream functions.
Topics: Adenylyl Cyclases; Cell Proliferation; Dictyostelium; Down-Regulation; GTP Phosphohydrolases; Mechanistic Target of Rapamycin Complex 1; Mechanistic Target of Rapamycin Complex 2; Signal Transduction; Sirolimus; Up-Regulation
PubMed: 31840789
DOI: 10.1387/ijdb.190245ak -
Genome Research Aug 2021development begins with single-cell starvation and ends with multicellular fruiting bodies. Developmental morphogenesis is accompanied by sweeping transcriptional...
development begins with single-cell starvation and ends with multicellular fruiting bodies. Developmental morphogenesis is accompanied by sweeping transcriptional changes, encompassing nearly half of the 13,000 genes in the genome. We performed time-series RNA-sequencing analyses of the wild type and 20 mutants to explore the relationships between transcription and morphogenesis. These strains show developmental arrest at different stages, accelerated development, or atypical morphologies. Considering eight major morphological transitions, we identified 1371 milestone genes whose expression changes sharply between consecutive transitions. We also identified 1099 genes as members of 21 regulons, which are groups of genes that remain coordinately regulated despite the genetic, temporal, and developmental perturbations. The gene annotations in these groups validate known transitions and reveal new developmental events. For example, DNA replication genes are tightly coregulated with cell division genes, so they are expressed in mid-development although chromosomal DNA is not replicated. Our data set includes 486 transcriptional profiles that can help identify new relationships between transcription and development and improve gene annotations. We show its utility by showing that cycles of aggregation and disaggregation in allorecognition-defective mutants involve dedifferentiation. We also show sensitivity to genetic and developmental conditions in two commonly used actin genes, and , and robustness of the gene. Finally, we propose that is a better mRNA quantitation standard because it is less sensitive to external conditions than commonly used standards. The data set is available for democratized exploration through the web application dictyExpress and the data mining environment Orange.
Topics: Dictyostelium; Morphogenesis; RNA, Messenger; Regulon; Software
PubMed: 34183452
DOI: 10.1101/gr.275496.121 -
Developmental Biology Jun 2015Cells grow, move, expand, shrink and die in the process of generating the characteristic shapes of organisms. Although the structures generated during development of the... (Review)
Review
Cells grow, move, expand, shrink and die in the process of generating the characteristic shapes of organisms. Although the structures generated during development of the social amoeba Dictyostelium discoideum look nothing like the structures seen in metazoan embryogenesis, some of the morphogenetic processes used in their making are surprisingly similar. Recent advances in understanding the molecular basis for directed cell migration, cell type specific sorting, differential adhesion, secretion of matrix components, pattern formation, regulation and terminal differentiation are reviewed. Genes involved in Dictyostelium aggregation, slug formation, and culmination of fruiting bodies are discussed.
Topics: Cell Shape; Chemotaxis; Cyclic AMP; Dictyostelium; Extracellular Matrix; Gene Expression Regulation, Developmental; Models, Biological; Morphogenesis
PubMed: 25872182
DOI: 10.1016/j.ydbio.2015.03.016 -
Biochimica Et Biophysica Acta. General... Jan 2017The extracellular matrix (ECM) is a dynamic complex of glycoproteins, proteoglycans, carbohydrates, and collagen that serves as an interface between mammalian cells and... (Review)
Review
BACKGROUND
The extracellular matrix (ECM) is a dynamic complex of glycoproteins, proteoglycans, carbohydrates, and collagen that serves as an interface between mammalian cells and their extracellular environment. Essential for normal cellular homeostasis, physiology, and events that occur during development, it is also a key functionary in a number of human diseases including cancer. The social amoeba Dictyostelium discoideum secretes an ECM during multicellular development that regulates multicellularity, cell motility, cell differentiation, and morphogenesis, and provides structural support and protective layers to the resulting differentiated cell types. Proteolytic processing within the Dictyostelium ECM leads to specific bioactive factors that regulate cell motility and differentiation.
SCOPE OF REVIEW
Here we review the structure and functions of the Dictyostelium ECM and its role in regulating multicellular development. The questions and challenges that remain and how they can be answered are also discussed.
MAJOR CONCLUSIONS
The Dictyostelium ECM shares many of the features of mammalian and plant ECM, and thus presents an excellent system for studying the structure and function of the ECM.
GENERAL SIGNIFICANCE
As a genetically tractable model organism, Dictyostelium offers the potential to further elucidate ECM functions, and to possibly reveal previously unknown roles for the ECM.
Topics: Dictyostelium; Disease; Extracellular Matrix; Extracellular Matrix Proteins; Humans; Protozoan Proteins; Signal Transduction
PubMed: 27693486
DOI: 10.1016/j.bbagen.2016.09.026 -
Current Opinion in Biotechnology Oct 2022The identification of novel platform organisms for the production and discovery of small molecules is of high interest for the pharmaceutical industry. In particular,... (Review)
Review
The identification of novel platform organisms for the production and discovery of small molecules is of high interest for the pharmaceutical industry. In particular, the structural complexity of most natural products with therapeutic potential restricts an industrial production since chemical syntheses often require complex multistep routes. The amoeba Dictyostelium discoideum can be easily cultivated in bioreactors due to its planktonic growth behavior and contains numerous polyketide and terpene synthase genes with only a few compounds being already elucidated. Hence, the amoeba both bears a wealth of hidden natural products and allows for the development of new bioprocesses for existing pharmaceuticals. In this mini review, we present D. discoideum as a novel platform for the production of complex secondary metabolites and discuss its suitability for industrial processes. We also provide initial insights into future bioprocesses, both involving bacterial coculture setups and for the production of plant-based pharmaceuticals.
Topics: Amoeba; Bacteria; Biological Products; Dictyostelium; Pharmaceutical Preparations
PubMed: 35944344
DOI: 10.1016/j.copbio.2022.102766 -
Methods in Molecular Biology (Clifton,... 2021GPCR signaling is the most prevailing molecular mechanism for detecting ambient signals in eukaryotes. Chemotactic cells use GPCR signaling to process chemical cues for...
GPCR signaling is the most prevailing molecular mechanism for detecting ambient signals in eukaryotes. Chemotactic cells use GPCR signaling to process chemical cues for directional migration over a broad concentration range and with high sensitivity. Dictyostelium discoideum is a classical model, in which the molecular mechanism underlying eukaryotic chemotaxis has been well studied. Here, we describe protocols to evaluate the spatiotemporal chemotactic responses of Dictyostelium discoideum by different microscopic observations combined with biochemical assays. First, two different chemotaxis assays are presented to measure the dynamic concentration ranges for different cell strains or chemotactic parameters. Next, live-cell imaging and biochemical assays are provided to detect the activities of GPCR and its partner heterotrimeric G proteins upon chemoattractant stimulation. Finally, a method for detecting how a cell deciphers chemical gradients is described.
Topics: Chemotactic Factors; Chemotaxis; Cyclic AMP; Dictyostelium; Green Fluorescent Proteins; Heterotrimeric GTP-Binding Proteins; Immunoprecipitation; Receptors, G-Protein-Coupled; Signal Transduction; Spatio-Temporal Analysis
PubMed: 34050483
DOI: 10.1007/978-1-0716-1258-3_27 -
The International Journal of... 2019When we set out to organize this Special Issue, we faced the difficult task of gathering together a large variety of topics with the unique commonality of having been...
When we set out to organize this Special Issue, we faced the difficult task of gathering together a large variety of topics with the unique commonality of having been studied in a single model organism, Dictyostelium discoideum. This apparent setback turned into a wonderful opportunity to learn about an organism as a whole, which provides a more complete understanding of life processes, their natural meaning and their changes during evolution. From studies dedicated almost exclusively to cell motility, differentiation and patterning, the versatility of D. discoideum has allowed in recent years the expansion of our knowledge to other areas, including cell biology and many others related to human diseases. The present collection of papers can be considered as a journey throughout the mechanisms of life, where D. discoideum acts as a very special tourist guide.
Topics: Body Patterning; Cell Biology; Cell Differentiation; Cell Movement; Dictyostelium; History, 20th Century; History, 21st Century; Models, Biological
PubMed: 31840771
DOI: 10.1387/ijdb.190275re -
The Journal of Eukaryotic Microbiology May 2016Evolved cooperation is stable only when the benefactor is compensated, either directly or through its relatives. Social amoebae cooperate by forming a mobile... (Review)
Review
Evolved cooperation is stable only when the benefactor is compensated, either directly or through its relatives. Social amoebae cooperate by forming a mobile multicellular body in which, about 20% of participants ultimately die to form a stalk. This benefits the remaining individuals that become hardy spores at the top of the stalk, together making up the fruiting body. In studied species with stalked migration, P. violaceum, D. purpureum, and D. giganteum, sorting based on clone identity occurs in laboratory mixes, maintaining high relatedness within the fruiting bodies. D. discoideum has unstalked migration, where cell fate is not fixed until the slug forms a fruiting body. Laboratory mixes show some degree of both spatial and genotype-based sorting, yet most laboratory fruiting bodies remain chimeric. However, wild fruiting bodies are made up mostly of clonemates. A genetic mechanism for sorting is likely to be cell adhesion genes tgrB1 and tgrC1, which bind to each other. They are highly variable, as expected for a kin discrimination gene. It is a puzzle that these genes do not cause stronger discrimination between mixed wild clones, but laboratory conditions or strong sorting early in the social stage diminished by later slug fusion could be explanations.
Topics: Amoeba; Animals; Biological Evolution; Cell Adhesion; Cell Movement; Dictyostelium; Fruiting Bodies, Fungal; Protozoan Proteins
PubMed: 26909677
DOI: 10.1111/jeu.12307 -
The International Journal of... 2020Simple organisms are preferred for understanding the molecular and cellular function(s) of complex processes. Dictyostelium discoideum is a lower eukaryote, a protist...
Simple organisms are preferred for understanding the molecular and cellular function(s) of complex processes. Dictyostelium discoideum is a lower eukaryote, a protist and a cellular slime mould, which has been in recent times used for various studies such as cell differentiation, development, cell death, stress responses etc. It is a soil amoeba (unicellular) that undertakes a remarkable, facultative shift to multicellularity when exposed to starvation and requires signal pathways that result in alteration of gene expression and finally show cell differentiation. The amoebae aggregate, differentiate and form fruiting bodies with two terminally differentiated cells: the dead stalk (non-viable) and dormant spores (viable). In India, starting from the isolation of Dictyostelium species to morphogenesis, cell signalling and social evolution has been studied with many more new research additions. Advances in molecular genetics make Dictyostelium an attractive model system to study cell biology, biochemistry, signal transduction and many more.
Topics: Animals; Biological Evolution; Biomedical Research; Cell Differentiation; Dictyostelium; Gene Expression Regulation; India; Models, Biological; Morphogenesis
PubMed: 32659023
DOI: 10.1387/ijdb.190208ss -
Journal of Cell Science Apr 2022Macropinocytosis mediates non-selective bulk uptake of extracellular fluid. It is the major route by which axenic Dictyostelium cells obtain nutrients and has emerged as...
Macropinocytosis mediates non-selective bulk uptake of extracellular fluid. It is the major route by which axenic Dictyostelium cells obtain nutrients and has emerged as a nutrient-scavenging pathway in mammalian cells. How environmental and cellular nutrient status modulates macropinocytic activity is not well understood. By developing a high-content imaging-based genetic screen in Dictyostelium discoideum we identified Slc15A, an oligopeptide transporter located at the plasma membrane and early macropinosome, as a novel macropinocytosis regulator. We show that deletion of slc15A but not two other related slc15 genes, leads to reduced macropinocytosis, reduced cell growth and aberrantly increased autophagy in cells grown in nutrient-rich medium. Expression of Slc15A protein or supplying cells with free amino acids rescues these defects. In contrast, expression of transport-defective Slc15A or supplying cells with amino acids in their di-peptide forms fails to rescue these defects. Therefore, Slc15A modulates the level of macropinocytosis by maintaining the intracellular availability of key amino acids through extraction of oligopeptides from the early macropinocytic pathway. We propose that Slc15A constitutes part of a positive feedback mechanism coupling cellular nutrient status and macropinocytosis. This article has an associated First Person interview with the first authors of the paper.
Topics: Animals; Dictyostelium; Endosomes; Humans; Mammals; Nutrients; Oligopeptides; Pinocytosis
PubMed: 35267018
DOI: 10.1242/jcs.259450