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Dictyostelium discoideum

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Dictyostelium discoideum

Dictyostelium discoideum
Fruiting bodies of D. discoideum
A migrating D. discoideum whose boundary is colored by curvature, scale bar: 5 µm, duration: 22 seconds
Scientific classification
Domain: Eukaryota
Kingdom: Protozoa
Phylum: Amoebozoa
Subphylum: Conosa
Infraphylum: Mycetozoa
Class: Dictyostelia
Order: Dictyosteliida
Family: Dictyosteliidae
Genus: Dictyostelium
Species: D. discoideum
Binomial name
Dictyostelium discoideum
Raper, 1935[1]

Dictyostelium discoideum is a species of soil-living amoeba belonging to the phylum Amoebozoa, infraphylum Mycetozoa. Commonly referred to as slime mold, D. discoideum is a eukaryote that transitions from a collection of unicellular amoebae into a multicellular slug and then into a fruiting body within its lifetime. Its unique asexual lifecycle consists of four stages: vegetative, aggregation, migration, and culmination. The lifecycle of D. discoideum is relatively short, which allows for timely viewing of all stages. The cells involved in the lifecycle undergo movement, chemical signaling, and development, which are applicable to human cancer research. The simplicity of its lifecycle makes D. discoideum a valuable model organism to study genetic, cellular, and biochemical processes in other organisms.

Natural habitat and diet

In the wild, D. discoideum can be found in soil and moist leaf litter. Its primary diet consists of amoebae of D. discoideum consume bacteria found in its natural habitat, which includes deciduous forest soil and decaying leaves.[2]

Lifecycle and reproduction

The lifecycle of D. discoideum begins as spores are released from a mature sorocarp (fruiting body). Myxamoebae hatch from the spores under warm and moist conditions. During their vegetative stage, the myxamoebae divide by mitosis as they feed on bacteria. The bacteria secrete folic acid, attracting the myxamoebae. When the supply of bacteria is depleted, the myxamoebae enter the aggregation stage.

During aggregation, starvation initiates the creation of a biochemical machinery that includes glycoproteins and adenylyl cyclase.[3] The glycoproteins allow for cell-cell adhesion, and adenylyl cyclase creates cyclic AMP. Cyclic AMP is secreted by the amoebae to attract neighboring cells to a central location. As they move toward the signal, they bump into each other and stick together by the use of glycoprotein adhesion molecules.

Lifecycle

The migration stage begins once the amoebae have formed a tight aggregate and the elongated mound of cells tip over to lie flat on the ground. The amoebae work together as a motile pseudoplasmodium, also known as a slug. The slug is about 2–4 mm long, composed of up to 100,000 cells,[4] and is capable of movement by producing a cellulose sheath in its anterior cells through which the slug moves.[5] Part of this sheath is left behind as a slimy trail as it moves toward attractants such as light, heat, and humidity in a forward-only direction.[5] Cyclic AMP and a substance called differentiation-inducing factor, help to form different cell types.[5] The slug becomes differentiated into prestalk and prespore cells that move to the anterior and posterior ends, respectively. Once the slug has found a suitable environment, the anterior end of the slug forms the stalk of the fruiting body and the posterior end forms the spores of the fruiting body.[5] Anterior-like cells, which have only been recently discovered, are also dispersed throughout the posterior region of the slug. These anterior-like cells form the very bottom of the fruiting body and the caps of the spores.[5] After the slug settles into one spot, the posterior end spreads out with the anterior end raised in the air, forming what is called the "Mexican hat", and the culmination stage begins.

The prestalk cells and prespore cells switch positions in the culmination stage to form the mature fruiting body.[5] The anterior end of the Mexican hat forms a cellulose tube, which allows the more posterior cells to move up the outside of the tube to the top, and the prestalk cells move down.[5] This rearrangement forms the stalk of the fruiting body made up of the cells from the anterior end of the slug, and the cells from the posterior end of the slug are on the top and now form the spores of the fruiting body. At the end of this 8– to 10-hour process, the mature fruiting body is fully formed.[5] This fruiting body is 1–2 mm tall and is now able to start the entire cycle over again by releasing the mature spores that become myxamoebae.

Sexual reproduction

In general, reproducing asexually, D. discoideum is still capable of sexual reproduction if certain conditions are met. When starved for their bacterial food supply, heterothallic or homothallic sexual development can occur, resulting in the formation of a diploid zygote.[6][7] Heterothallic mating occurs when two amoebae of different mating types are present in a dark and wet environment, where they can fuse during aggregation to form a giant cell. The giant cell then engulfs the other cells in the aggregate and encase the whole aggregate in a thick, cellulose wall to protect it. This is known as a macrocyst. Inside the macrocyst, the giant cell divides first through meiosis, then through mitosis to produce many haploid amoebae that will be released to feed as normal amoebae would. Homothallic D. discoideum strains AC4 and ZA3A are also able to produce macrocysts.[8] Each of these strains, unlike heterothallic strains, likely express both mating type alleles (matA and mata). While sexual reproduction is possible, it is very rare to see successful germination of a D. discoideum macrocyst under laboratory conditions. Nevertheless, recombination is widespread within D. discoideum natural populations, indicating that sex is likely an important aspect of their lifecycle.[7]

Use as a model organism

Because of the simple lifecycle of D. discoideum, it is commonly used as a gene knockout.[10]

The [11] These cell fates depend on their environment and pattern formation. Therefore, the organism is an excellent model for studying cell differentiation.

D. discoideum exhibiting chemotaxis through aggregation

[12]

The use of cAMP as a chemotactic agent is not established in any other organism. In developmental biology, this is one of the comprehensible examples of chemotaxis.[5]

[13]

[3] As they differentiate, they form vacuoles and enlarge, lifting up the prespore cells. The stalk cells undergo apoptosis and die as the prespore cells are lifted high above the substrate. The prespore cells then become spore cells, each one becoming a new myxamoeba upon dispersal.[5] This is an example of how apoptosis is used in the formation of a reproductive organ, the mature fruiting body.

A recent major contribution from Dictyostelium research has come from new techniques allowing the activity of individual genes to be visualised in living cells.[14] This has shown that transcription occurs in "bursts" or "pulses" ([15] Defects in DNA repair lead to devastating human cancers, so the ability to study human repair proteins in a simple tractable model will prove invaluable.

Lab cultivation

This organism's ability to be easily cultivated in the laboratory[5] adds to its appeal as a model organism. While D. discoideum can be grown in liquid culture, it is usually grown in Petri dishes containing nutrient agar and the surfaces are kept moist. The cultures grow best at 22–24°C (room temperature). D. discoideum feed primarily on E. coli, which is adequate for all stages of the lifecycle. When the food supply is diminished, the myxamoebae aggregate to form pseudoplasmodia. Soon, the dish is covered with various stages of the lifecycle. Checking the dish often allows for detailed observations of development. The cells can be harvested at any stage of development and grown quickly.

While cultivating D. discordium in a laboratory, it is important to take into account its behavioral responses. For example, it has an affinity toward light, higher temperatures, high humidity, low ionic concentrations, and the acidic side of the pH gradient. Experiments are often done to see how manipulations of these parameters hinder, stop, or accelerate development. Variations of these parameters can alter the rate and viability of culture growth. Also, the fruiting bodies, being that this is the tallest stage of development, are very responsive to air currents and physical stimuli. It is unknown if there is a stimulus involved with spore release.

Protein expression studies

Detailed analysis of protein expression in Dictyostelium has been hampered by large shifts in the protein expression profile between different developmental stages and a general lack of commercially available antibodies for Dictyostelium antigens.[16] In 2013, a group at the Beatson West of Scotland Cancer Centre reported an antibody-free protein visualization standard for immunoblotting based on detection of MCCC1 using streptavidin conjugates.[17]

"Farming"

A 2011 report in Nature published findings that demonstrated a "primitive farming behaviour" in D. discoideum colonies.[18][19] Described as a "symbiosis" between D. discoideum and bacterial prey, about one-third of wild-collected D. discoideum colonies engaged in the "husbandry" of the bacteria when the bacteria were included within the slime mold fruiting bodies.[19] The incorporation of the bacteria into the fruiting bodies allows the "seeding" of the food source at the location of the spore dispersal, which is particularly valuable if the new location is low in food resources.[19] Colonies produced from the "farming" spores typically also show the same behavior when sporulating. This incorporation has a cost associated with it: Those colonies that do not consume all of the prey bacteria produce smaller spores that cannot disperse as widely. In addition, much less benefit exists for bacteria-containing spores that land in a food-rich region. This balance of the costs and benefits of the behavior may contribute to the fact that a minority of D. discoideum colonies engage in this practice.[18][19]

D. discoideum is known for eating Gram-positive, as well as Gram-negative bacteria, but some of the phagocytized bacteria, including some human pathogens,[20] are able to live in the amoebae and exit without killing the cell. When they enter the cell, where they reside, and when they leave the cell are not known. The research is not yet conclusive but it is possible to draw a general lifecycle of D. discoideum adapted for farmer clones to better understand this symbiotic process.
Lifecycle of farmer D. discoideum

In the picture, one can see the different stages. First, in the starvation stage, bacteria are enclosed within D. discoideum,[20] after entry into amoebae, in a phagosome the fusion with lysosomes is blocked and these unmatured phagosomes are surrounded by host cell organelles such as mitochondria, vesicles, and a multilayer membrane derived from the rough endoplasmic reticulum (RER) of amoebae. The role of the RER in the intracellular infection is not known, but the RER is not required as a source of proteins for the bacteria.[21] The bacteria reside within these phagosomes during the aggregation and the multicellular development stages. The amoebae preserve their individuality and each amoeba has its own bacterium. During the culmination stage, when the spores are produced, the bacteria pass from the cell to the sorus with the help of a cytoskeletal structure that prevents host cell destruction.[22] Some results suggest the bacteria exploit the exocytosis without killing the cell.[22] Free-living amoebae seem to play a crucial role for persistence and dispersal of some pathogens in the environment. Transient association with amoebae has been reported for a number of different bacteria, including Legionella pneumophila, many Mycobacterium species, Francisella tubarensis, and Escherichia coli, among others.[21] Agriculture seems to play a crucial role for pathogens' survival, as they can live and replicate inside D. discoideum, making husbandry. Nature’s report has made an important advance in the knowledge of amoebic behavior, and the famous Spanish phrase translated as “you are more stupid than an amoeba” is losing the sense because amoebae are an excellent example of social behavior with an amazing coordination and sense of sacrifice for the benefit of the species.

Current applications in research

Several D. discoideum genes are homologous to human genes, making them a useful model organism. The entire genome was sequenced in a model organism database called dictyBase. Using these sequences, scientists are now able to run more complex experiments, especially on human diseases. These slime molds are used to test anticancer drugs, immune-cell diseases, and bacterial intracellular pathogenesis. Also, Dictyostelium was established to use DNA methylation for regulating gene expression.

Individual cell behavior accounts for many phases of health and disease. This is portrayed in D. discoideum in many different ways. Cytokinesis acts as part of immune response, tissue maintenance, and cancer, in the form of cell proliferation. Chemotaxis deals with inflammation, arthritis, asthma, lymphocyte trafficking, and axon guidance. Phagocytosis is used in immune surveillance and antigen presentation, while cell-type determination, cell sorting, and pattern formation are basic features of embryogenesis.

The Legionella genus of bacteria includes the species that causes legionnaire's disease in humans. D. discoideum is also a host for Legionella and is a suitable model for studying the infection process.[23] Specifically, D. discoideum shares with mammalian host cells a similar cytoskeleton and cellular processes relevant to Legionella infection, including phagocytosis, membrane trafficking, endocytosis, vesicle sorting, and chemotaxis.

Much research has been done to better understand the behavioral responses of D. discoideum, the slug form that has an array of behavioral traits. Although it lacks sensory cells and organs, it has a keen response to external stimuli, such as temperature and light. Over 100,000 individual amoebae are attracted to one another through chemotaxis. However, light is directly related to the cAMP cell-cell signaling in chemotaxis. Within the D. discoideum, the light causes cAMP to be released from the slug tip, thus speeding up and directing movement toward the light source. D. discoideum also prefers a slightly acidic pH. When intracellular pH is increased, the result is increased locomotion during chemotaxis. The movement of the slug is also increased because the movement of each individual cell has increased.

Classification and phylogeny

In older classifications, Dictyostelium was placed in the defunct polyphyletic class Acrasiomycetes. This was a class of cellular slime molds, which was characterized by the aggregation of individual amoebae into a multicellular fruiting body, making it an important factor that related the acrasids to the dictyostelids.[24]

More recent genomic studies have shown that Dictyostelium has maintained more of its ancestral genome diversity than plants and animals, although proteome-based phylogeny confirms that amoebozoa diverged from the animal–fungal lineage after the plant–animal split.[25] Subclass Dictyosteliidae, order Dictyosteliales is a monophyletic assemblage within the Mycetozoa, a group that includes the protostelid, dictyostelid, and myxogastrid slime molds. Elongation factor-1α (EF-1α) data analyses support Mycetozoa as a monophyletic group, though rRNA trees place it as a polyphyletic group. Further, these data support the idea that the dictyostelid and myxogastrid are more closely related to each other than they are the protostelids. EF-1α analysis also placed the Mycetozoa as the immediate outgroup for the animal-fungal clade.[26] Latest phylogenetic data place dictyostelids firmly within supergroup Amoebozoa, along with myxomycetes. Meanwhile, protostelids have turned out to be polyphyletic, their stalked fruiting bodies a convergent feature of multiple unrelated lineages.[27]

Genome

The D. discoideum genome sequencing project was completed and published in 2005 by an international collaboration of institutes. This was the first free-living protozoan genome to be fully sequenced. D. discoideum consists of a 34-Mb haploid genome with a base composition of 77% [A+T] and contains six chromosomes that encode around 12,500 proteins.[2] Sequencing of the D. discoideum genome provides a more intricate study of its cellular and developmental biology.

Tandem repeats of trinucleotides are very abundant in this genome; one class of the genome is clustered, leading researchers to believe it serves as centromeres. The repeats correspond to repeated sequences of amino acids and are thought to be expanded by nucleotide expansion.[2] Expansion of trinucleotide repeats also occurs in humans, in general leading to many diseases. Learning how D. discoideum cells endure these amino acid repeats may provide insight to allow humans to tolerate them.

Every genome sequenced plays an important role in identifying genes that have been gained or lost over time. Comparative genomic studies allow for comparison of eukaryotic genomes. A phylogeny based on the proteome showed that the amoebozoa deviated from the animal-fungal lineage after the plant-animal split.[2] The D. discoideum genome is noteworthy because its many encoded proteins are commonly found in fungi, plants, and animals.[2]

References

  1. ^
  2. ^ a b c d e
  3. ^ a b c Gilbert S.F. 2006. Developmental Biology. 8th ed. Sunderland (MA):Sinauer p. 36-39.
  4. ^
  5. ^ a b c d e f g h i j k l Tyler M.S. 2000. Developmental Biology: A guide for experimental study. 2nd ed. Sunderland (MA): Sinauer. p. 31-34. ISBN 0-87893-843-5
  6. ^
  7. ^ a b
  8. ^
  9. ^ Dictybase, About Dictyostelium. [Online] (1, May, 2009). http://dictybase.org/
  10. ^ Dilip K. Nag, Disruption of Four Kinesin Genes in Dictyostelium. [Online] (22, April, 2008). http://ukpmc.ac.uk/articlerender.cgi?artid=1529371
  11. ^
  12. ^ Dusenbery, David B. (1996). “Life at Small Scale”, pp.174-175. Scientific American Library, New York. ISBN 0-7167-5060-0.
  13. ^ Dusenbery, David B. (1996). “Life at Small Scale”, pp.108-109. Scientific American Library, New York. ISBN 0-7167-5060-0.
  14. ^
  15. ^
  16. ^
  17. ^
  18. ^ a b "Amoebas show primitive farming behaviour as they travel", BBC News, 19 January 2011
  19. ^ a b c d
  20. ^ a b
  21. ^ a b
  22. ^ a b
  23. ^ Bruhn H. 2008. Dictyostelium, a tractable model host organism for Legionella. In: Heuner K, Swanson M, editors. Legionella: Molecular Microbiology. Norwich (UK): Caister Academic Press. ISBN 978-1-904455-26-4
  24. ^
  25. ^
  26. ^
  27. ^

Further reading

External links

  • Dictyostelium discoideumModel Organisms for Biomedical Research:
  • at MetaMicrobe: taxonomy, facts, ontologies, and referencesD. discoideum
  • DictyBase
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