''Physarum polycephalum'', an
acellular slime mold
Slime mold or slime mould is an informal name given to a polyphyletic assemblage of unrelated eukaryotic organisms in the Stramenopiles, Rhizaria, Discoba, Amoebozoa and Holomycota clades. Most are near-microscopic; those in the Myxogastria ...
or
myxomycete popularly known as "the blob", is a
protist
A protist ( ) or protoctist is any eukaryotic organism that is not an animal, land plant, or fungus. Protists do not form a natural group, or clade, but are a paraphyletic grouping of all descendants of the last eukaryotic common ancest ...
with diverse cellular forms and broad geographic distribution. The “acellular” moniker derives from the plasmodial stage of the
life cycle: the
plasmodium
''Plasmodium'' is a genus of unicellular eukaryotes that are obligate parasites of vertebrates and insects. The life cycles of ''Plasmodium'' species involve development in a Hematophagy, blood-feeding insect host (biology), host which then inj ...
is a bright yellow macroscopic
multinucleate
Multinucleate cells (also known as multinucleated cells or polynuclear cells) are eukaryotic cells that have more than one nucleus, i.e., multiple nuclei share one common cytoplasm. Mitosis in multinucleate cells can occur either in a coordinate ...
coenocyte
A coenocyte () is a multinucleate cell which can result from multiple nuclear divisions without their accompanying cytokinesis, in contrast to a syncytium, which results from cellular aggregation followed by dissolution of the cell membranes i ...
shaped in a network of interlaced tubes. This stage of the life cycle, along with its preference for damp shady habitats, likely contributed to the original mischaracterization of the organism as a
fungus
A fungus (: fungi , , , or ; or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified as one ...
. ''P. polycephalum'' is used as a
model organism
A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms. Mo ...
for research into
motility
Motility is the ability of an organism to move independently using metabolism, metabolic energy. This biological concept encompasses movement at various levels, from whole organisms to cells and subcellular components.
Motility is observed in ...
,
cellular differentiation
Cellular differentiation is the process in which a stem cell changes from one type to a differentiated one. Usually, the cell changes to a more specialized type. Differentiation happens multiple times during the development of a multicellula ...
,
chemotaxis
Chemotaxis (from ''chemical substance, chemo-'' + ''taxis'') is the movement of an organism or entity in response to a chemical stimulus. Somatic cells, bacteria, and other single-cell organism, single-cell or multicellular organisms direct thei ...
,
cellular compatibility, and the
cell cycle
The cell cycle, or cell-division cycle, is the sequential series of events that take place in a cell (biology), cell that causes it to divide into two daughter cells. These events include the growth of the cell, duplication of its DNA (DNA re ...
. It is commonly cultivated.
Life cycle and characteristics
The two vegetative cell types,
amoebae
An amoeba (; less commonly spelled ameba or amœba; : amoebas (less commonly, amebas) or amoebae (amebae) ), often called an amoeboid, is a type of cell or unicellular organism with the ability to alter its shape, primarily by extending and r ...
and
plasmodia, differ markedly in morphology, physiology and behavior. Amoebae are
microorganism
A microorganism, or microbe, is an organism of microscopic scale, microscopic size, which may exist in its unicellular organism, single-celled form or as a Colony (biology)#Microbial colonies, colony of cells. The possible existence of unseen ...
s, typically
haploid
Ploidy () is the number of complete sets of chromosomes in a cell (biology), cell, and hence the number of possible alleles for Autosome, autosomal and Pseudoautosomal region, pseudoautosomal genes. Here ''sets of chromosomes'' refers to the num ...
, that live primarily in the soil, where they
phagocytose
Phagocytosis () is the process by which a cell uses its plasma membrane to engulf a large particle (≥ 0.5 μm), giving rise to an internal compartment called the phagosome. It is one type of endocytosis. A cell that performs phagocytosis is c ...
bacteria
Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
. In the laboratory, amoebae are grown on
lawns of live or dead ''
Escherichia coli
''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly fo ...
'' on nutrient
agar
Agar ( or ), or agar-agar, is a jelly-like substance consisting of polysaccharides obtained from the cell walls of some species of red algae, primarily from " ogonori" and " tengusa". As found in nature, agar is a mixture of two components, t ...
plates, where they can multiply indefinitely.
Axenic culture of amoebae was achieved through selection of mutants capable of axenic growth. Under conditions of starvation or desiccation, the amoebae differentiate reversibly into dormant spores with cell walls. When immersed in water, amoebae differentiate reversibly into flagellated cells, which involves a major reorganization of the cytoskeleton.
The plasmodium is typically
diploid
Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Here ''sets of chromosomes'' refers to the number of maternal and paternal chromosome copies, ...
and propagates via growth and nuclear division without
cytokinesis
Cytokinesis () is the part of the cell division process and part of mitosis during which the cytoplasm of a single eukaryotic cell divides into two daughter cells. Cytoplasmic division begins during or after the late stages of nuclear division ...
, resulting in the macroscopic multinucleate syncytium; in other words, a large single cell with multiple nuclei. While nutrients are available, the network-shaped plasmodium can grow to a foot or more in diameter. Like amoebae, the plasmodium can consume whole microbes, but also readily grows axenically in liquid cultures, nutrient agar plates and on nutrient-moistened surfaces. When nutrients are provided uniformly, the nuclei in the plasmodium divide synchronously, accounting for the interest in using ''P. polycephalum'' as a model organism to study the cell cycle, or more specifically the nuclear division cycle. When the plasmodium is starved, it has two alternative developmental pathways. In the dark, the plasmodium typically differentiates reversibly into a dormant “sclerotium” (the same term is used for
dormant forms of fungal mycelia, but the myxomycete sclerotium is a very different structure). When exposed to light, the starving plasmodium differentiates irreversibly into sporangia that are distinguished from other ''Physarum'' species by their multiple heads (hence ''polycephalum''). Meiosis occurs during spore development, resulting in haploid dormant spores. Upon exposure to moist nutrient conditions, the spores develop into amoebae, or, in aqueous suspension, into flagellates. The life cycle is completed when haploid amoebae of different mating types fuse to form a diploid zygote that then develops by growth and nuclear division in the absence of cytokinesis into the multinucleate plasmodium.
In laboratory strains carrying a mutation at the ''matA''
mating-type locus, the differentiation of ''P. polycephalum'' plasmodia can occur without the fusion of amoebae, resulting in haploid plasmodia that are morphologically indistinguishable from the more typical diploid form. This enables easier genetic analysis of plasmodial traits that would otherwise require backcrossing to achieve homozygosity for analysis of recessive mutations in diploids. Sporangia from haploid plasmodia generate spores with low fertility, and it is assumed that viable spores develop from meiosis of rare diploid nuclei in the otherwise haploid ''P. polycephalum'' plasmodia.
Apogamic development can also occur in nature in various species of myxomycetes. In the figure of the ''P. polycephalum'' life cycle, the typical haploid-diploid sexual cycle is depicted in the outer circuit and the apogamic cycle in the inner circuit. Note that an apogamic amoeba retains its ''matA1'' mating type specificity and can still fuse sexually with an amoeba of a different mating type to form a diploid heterozygous plasmodium—another characteristic that facilitates genetic analysis.
As the life cycle diagram indicates, amoebae and plasmodia differ markedly in their developmental potential. A remarkable further difference is the mechanism of mitosis. Amoebae exhibit “open mitosis” during which the nuclear membrane breaks down, as is typical of animal cells, before reassembling after
telophase
Telophase () is the final stage in both meiosis and mitosis in a eukaryotic cell. During telophase, the effects of prophase and prometaphase (the nucleolus and nuclear membrane disintegrating) are reversed. As chromosomes reach the cell poles, ...
. Plasmodia exhibit “closed mitosis” during which the nuclear membrane remains intact. This presumably prevents nuclear fusion from occurring during mitosis in the multinucleate syncytium. In support of this inference, mutant amoebae defective in cytokinesis develop into multinucleate cells, and nuclear fusions during mitosis are common in these mutants.
Cytoplasmic streaming
The plasmodium of myxomycetes, and especially that of ''Physarum polycephalum'' is known for its cytoplasmic streaming. The cytoplasm undergoes a shuttle flow rhythmically flowing back and forth, changing direction typically every 100 seconds. Flows can reach speeds of up to 1mm/s. Within the tubular network flows arise due to the cross-sectional contractions of the tubes that are generated by the contraction and relaxation of the membranous outer layer of the tubes enriched with
acto-myosin cortex. In stationary plasmodia, tubular contractions are spatially organized across the entire plasmodium in a peristaltic wave.
Cytoplasmic streaming is likely to contribute to plasmodium migration. Here, contraction patterns are observed to correlate with migration speed. For dumbbell-shaped microplasmodia, often termed Amoeboid plasmodia, stiffening of the cortex in the rear versus the front seems instrumental in breaking the symmetry for the contraction wave to translate into migration.
Cytoplasmic flows enable long-ranged transport and dispersion of molecules within the cytoplasm. The physical mechanism employed here is
Taylor dispersion. Under starvation the organism may reorganize its network morphology and thereby enhance its dispersion capabilities. In fact, the flows are even hijacked to transport signals throughout the plasmodium network. It is likely that the feedback of transported signals on tube size underlies ''Physarums capability to find the shortest path through a maze.
Situational behavior
''P. polycephalum'' not only can solve these computational problems but also exhibits some form of
memory
Memory is the faculty of the mind by which data or information is encoded, stored, and retrieved when needed. It is the retention of information over time for the purpose of influencing future action. If past events could not be remembe ...
. By repeatedly making the test environment of a specimen of ''P. polycephalum'' cold and dry for 60 minute intervals,
Hokkaido University
, or , is a public research university in Sapporo, Hokkaido, Japan. Founded in 1918, it is the fifth-oldest government-authorised university in Japan and one of the former Imperial Universities.
The university finds its roots in Sapporo A ...
biophysicists discovered that the slime mold appears to anticipate the pattern by reacting to the conditions when they did not repeat the conditions for the next interval. Upon repeating the conditions, it would react to expect the 60 minute intervals, as well as testing with 30 and 90 minute intervals.
''P. polycephalum'' has also been shown to dynamically re-allocate to apparently maintain constant levels of different nutrients simultaneously.
In one particular instance, a specimen placed at the center of a
Petri dish
A Petri dish (alternatively known as a Petri plate or cell-culture dish) is a shallow transparent lidded dish that biologists use to hold growth medium in which cells can be cultured,R. C. Dubey (2014): ''A Textbook Of Biotechnology For Class- ...
spatially re-allocated over combinations of food sources that each had different
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
-
carbohydrate
A carbohydrate () is a biomolecule composed of carbon (C), hydrogen (H), and oxygen (O) atoms. The typical hydrogen-to-oxygen atomic ratio is 2:1, analogous to that of water, and is represented by the empirical formula (where ''m'' and ''n'' ...
ratios. After 60 hours, the slime mold area over each food source was measured. For each specimen, the results were consistent with the hypothesis that the amoeba would balance total protein and carbohydrate intake to reach particular levels that were invariant to the actual ratios presented to the slime mold.
As the slime mold does not have any nervous system that could explain these intelligent behaviours, there has been considerable interdisciplinary interest in understanding the rules that govern its behaviour. Scientists are trying to model the slime mold using a number of simple, distributed rules. For example, ''P. polycephalum'' has been modeled as a set of
differential equations inspired by electrical networks. This model can be shown to be able to compute shortest paths. A very similar model can be shown to solve the
Steiner tree problem
In combinatorial mathematics, the Steiner tree problem, or minimum Steiner tree problem, named after Jakob Steiner, is an umbrella term for a class of problems in combinatorial optimization. While Steiner tree problems may be formulated in a ...
.
However, these models are externally consistent but not internally explanatory, and as is usual for modelling they simplify — in this case assuming
conservation of energy
The law of conservation of energy states that the total energy of an isolated system remains constant; it is said to be Conservation law, ''conserved'' over time. In the case of a Closed system#In thermodynamics, closed system, the principle s ...
. To build more realistic models, more data about the slime mold's network construction needs to be gathered. To this end, researchers are analysing the network structure of lab-grown ''P. polycephalum''.
In a book
and several preprints that have not been peer-reviewed,
[
] it has been claimed that because plasmodia appear to react in a consistent way to stimuli, they are the "ideal substrate for future and emerging
bio-computing devices".
An outline has been presented showing how it may be possible to precisely point, steer and cleave plasmodium using light and food sources,
especially
Valerian root. Moreover, it has been reported that plasmodia can be made to form
logic gate
A logic gate is a device that performs a Boolean function, a logical operation performed on one or more binary inputs that produces a single binary output. Depending on the context, the term may refer to an ideal logic gate, one that has, for ...
s,
enabling the construction of biological computers. In particular, plasmodia placed at entrances to special geometrically shaped mazes would emerge at exits of the maze that were consistent with
truth table
A truth table is a mathematical table used in logic—specifically in connection with Boolean algebra, Boolean functions, and propositional calculus—which sets out the functional values of logical expressions on each of their functional arg ...
s for certain primitive logic connectives. However, as these constructions are based on theoretical models of the slime mold, in practice these results do not scale to allow for actual computation. When the primitive logic gates are connected to form more complex functions, the plasmodium ceased to produce results consistent with the expected truth tables.
Even though complex computations using ''Physarum'' as a substrate are currently not possible, researchers have successfully used the organism's reaction to its environment in a USB sensor
and to control a robot.
Innate immunity
''P. polycephalum'' produces its own antiviral substances. Mayhew & Ford 1971 find an extract of ''P. polycephalum'' prevents some
crop diseases: ''
Tobacco mosaic virus
Tobacco mosaic virus (TMV) is a positive-sense single-stranded RNA virus species in the genus '' Tobamovirus'' that infects a wide range of plants, especially tobacco and other members of the family Solanaceae. The infection causes characteris ...
'' and ''
tobacco ringspot virus'' are inhibited by a product of ''P. polycephalum''. Both ''
Nicotiana tabacum
''Nicotiana tabacum'', or cultivated tobacco, is an annually grown herbaceous plant of the genus ''Nicotiana''. ''N. tabacum'' is the most commonly grown species in the genus ''Nicotiana,'' as the plant's leaves are commercially harvested to be ...
'' and the beans ''
Phaseolus vulgaris
''Phaseolus vulgaris'', the common bean,, is a herbaceous annual plant grown worldwide for its edible dry seeds or green, unripe pods. Its leaf is also occasionally used as a vegetable and the straw as fodder. Its botanical classification, alo ...
'' and ''
Vigna sinensis'' suffered almost no
lesion
A lesion is any damage or abnormal change in the tissue of an organism, usually caused by injury or diseases. The term ''Lesion'' is derived from the Latin meaning "injury". Lesions may occur in both plants and animals.
Types
There is no de ...
ing ''in vitro'' from ''TMV'' or ''TRSV'' when treated with a ''P. polycephalum'' extract. However, the ''
southern bean mosaic virus'' was unaffected.
Mitochondrial DNA
''P. polycephalum'' exhibits a complex
mitochondrial
A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used ...
DNA (
mtDNA
Mitochondrial DNA (mtDNA and mDNA) is the DNA located in the mitochondria organelles in a eukaryotic cell that converts chemical energy from food into adenosine triphosphate (ATP). Mitochondrial DNA is a small portion of the DNA contained in ...
) structure that is distinctive in both its composition and functional mechanisms. The mtDNA of Physarum polycephalum is characterized by its unique
RNA editing
RNA editing (also RNA modification) is a molecular process through which some cells can make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase. It occurs in all living organisms ...
process.
The mtDNA of ''P. polycephalum'' comprises up to 81 genes, of which a significant number are
cryptogenes that require RNA editing for functional expression. These employ the co-transcriptional RNA editing process known as MICOTREM (
Mitochondrial
Insertional
Cotranscriptional
RNA
Editing in
Myxomycetes). This process is crucial for the expression of 43 cryptogenes within the mtDNA. Unlike other organisms where RNA editing typically involves
guide RNAs, MICOTREM involves the insertional editing of RNA, where specific non-templated nucleotides are added to the RNA transcript. The mitochondrial
RNA polymerase
In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template.
Using the e ...
facilitates this process by adding
cytidines,
uridines, or a subset of
dinucleotides to the nascent RNA transcript at specific editing sites. The exact mechanism and specification of editing sites in MICOTREM are complex and not fully understood, with ongoing research focusing on the potential mechanisms involving RNA-DNA duplex formation and the role of mitochondrial RNA polymerase.
The mtDNA in this organism also includes sequences derived from a linear mitochondrial
plasmid
A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria and ...
.
See also
*
Sedolisin
*
Physarum polycephalum ribonuclease
References
Sources
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External links
* (in French, with English subtitles available)
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* (Season 47 Episode 12 , 53m 17s)
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{{Authority control
Physaraceae
Myxogastria species
Protists described in 1822