Two cell-counting factors regulate the aggregate size of the cellular slime mold Dictyostelium discoideum

Molecular Characterization of Ancient Prosaposin-like Proteins from the Protist Dictyostelium discoideum

To combat the permanent exposure to potential pathogens every organism relies on an immune system. Important factors in innate immunity are antimicrobial peptides (AMPs) that are structurally highly diverse. Some AMPs are known to belong to the saposin-like proteins (SAPLIPs), a group of polypeptides with a broad functional spectrum. The model organism Dictyostelium discoideum possesses a remarkably large arsenal of potential SAPLIPs, which are termed amoebapore-like peptides (Apls), but the knowledge about these proteins is very limited. Here, we report about the biochemical characterization of AplE1, AplE2, AplK1, and AplK2, which are derived from the two precursor proteins AplE and AplK, thereby resembling prosaposins of vertebrates. We produced these Apls as recombinant polypeptides in Escherichia coli using a self-splicing intein to remove an affinity tag used for purification. All recombinant Apls exhibited pore-forming activity in a pH-dependent manner, as evidenced by liposome depolarization, showing higher activities the more acidic the setting was. Lipid preference was detected for negatively charged phospholipids and in particular for cardiolipin. Antimicrobial activity against various bacteria was found to be inferior in classical microdilution assays. However, all of the Apls studied permeabilized the cytoplasmic membrane of live Bacillus subtilis. Collectively, we assume that the selected Apls interact by their cationic charge with negatively charged bacterial membranes in acidic environments such as phagolysosomes and eventually lyse the target cells by pore formation.

Investigating the Role of Translationally Control Tumor Protein in Growth, Development and Differentiation of Dictyostelium discoideum

Translationally controlled tumor protein (TCTP) is a multifunctional protein implicated in various types of cellular processes involving growth and development of an organism. Here, we identified tctp gene in Dictyostelium discoideum and unraveled its function. The sequence analysis of D. discoideum TCTP (DdTCTP) showed its conservation among eukaryotes. Transcript of DdTCTP was highly expressed at the initial time points of development and protein is localized both in the cytoplasm and nucleus. Disruption of tctp was achieved by BSR cassette using double homologous recombination method. Abrogation of tctp resulted in reduced cell proliferation but increased cell size. Additionally, development was delayed by 4 h wherein small-sized aggregates and fruiting bodies were produced by tctp^– cells while larger aggregates and fruiting bodies were produced by tctp^OE cells concordant with the fact that TCTP regulates prestalk/prespore ratio and cell-type differentiation. tctp^– cells produced round spores with reduced viability and stalk cells are arranged in septate pattern as compared to polyhedral manner of wild type. Abrogation of tctp resulted in aberrant localization of cell type specific markers and show low proclivity toward prespore/spore region, in presence of wild type cells.

Secretion and function of Cln5 during the early stages of Dictyostelium development

Mutations in CLN5 cause neuronal ceroid lipofuscinosis (NCL), a currently untreatable neurodegenerative disorder commonly known as Batten disease. Several genetic models have been generated to study the function of CLN5, but one limitation has been the lack of a homolog in lower eukaryotic model systems. Our previous work revealed a homolog of CLN5 in the social amoeba Dictyostelium discoideum. We used a Cln5-GFP fusion protein to show that the protein is secreted and functions as a glycoside hydrolase in Dictyostelium. Importantly, we also revealed this to be the molecular function of human CLN5. In this study, we generated an antibody against Cln5 to show that the endogenous protein is secreted during the early stages of Dictyostelium development. Like human CLN5, the Dictyostelium homolog is glycosylated and requires this post-translational modification for secretion. Cln5 secretion bypasses the Golgi complex, and instead, occurs via an unconventional pathway linked to autophagy. Interestingly, we observed co-localization of Cln5 and GFP-Cln3 as well as increased secretion of Cln5 and Cln5-GFP in cln3- cells. Loss of Cln5 causes defects in adhesion and chemotaxis, which intriguingly, has also been reported for Dictyostelium cells lacking Cln3. Finally, autofluorescence was detected in cln5- cells, which is consistent with observations in mammalian systems. Together, our data support a function for Cln5 during the early stages of multicellular development, provide further evidence for the molecular networking of NCL proteins, and provide insight into the mechanisms that may underlie CLN5 function in humans.

A critical-like collective state leads to long-range cell communication in Dictyostelium discoideum aggregation

The transition from single-cell to multicellular behavior is important in early development but rarely studied. The starvation-induced aggregation of the social amoeba Dictyostelium discoideum into a multicellular slug is known to result from single-cell chemotaxis towards emitted pulses of cyclic adenosine monophosphate (cAMP). However, how exactly do transient, short-range chemical gradients lead to coherent collective movement at a macroscopic scale? Here, we developed a multiscale model verified by quantitative microscopy to describe behaviors ranging widely from chemotaxis and excitability of individual cells to aggregation of thousands of cells. To better understand the mechanism of long-range cell—cell communication and hence aggregation, we analyzed cell—cell correlations, showing evidence of self-organization at the onset of aggregation (as opposed to following a leader cell). Surprisingly, cell collectives, despite their finite size, show features of criticality known from phase transitions in physical systems. By comparing wild-type and mutant cells with impaired aggregation, we found the longest cell—cell communication distance in wild-type cells, suggesting that criticality provides an adaptive advantage and optimally sized aggregates for the dispersal of spores.

A multiscale model and imaging data show that cells of the slime mold Dictyostelium discoideum maximize their cell—cell communication range during aggregation by a critical-like state known from phase transitions in physical systems.

Cells are often coupled to each other in cell collectives, such as aggregates during early development, tissues in the developed organism, and tumors in disease. How do cells communicate over macroscopic distances much larger than the typical cell—cell distance to decide how they should behave? Here, we developed a multiscale model of social amoeba, spanning behavior from individuals to thousands of cells. We show that local cell—cell coupling via secreted chemicals may be tuned to a critical value, resulting in emergent long-range communication and heightened sensitivity. Hence, these aggregates are remarkably similar to bacterial biofilms and neuronal networks, all communicating in a pulselike fashion. Similar organizing principles may also aid our understanding of the remarkable robustness in cancer development.

Response of Dictyostelium discoideum to UV-C and involvement of poly (ADP-ribose) polymerase

OBJECTIVES

Radiation and chemical mutagens are direct DNA-damaging agents and ultraviolet (UV) radiation is frequently used in biological studies. Consequent to ozone depletion, UV-C could become a great challenge to living organisms on earth, in the near future. The present study has focused on the role of poly (ADP-ribose) polymerase (PARP) during UV-C-induced growth and developmental changes in Dictyostelium discoideum, a phylogenetically important unicellular eukaryote.

MATERIALS AND METHODS

Dictyostelium discoideum cells were exposed to different doses of UV-C and PARP activity, and effects of its inhibition were studied. Expression of developmentally regulated genes yakA, car1, aca, csA, regA, ctnA, ctnB, gp24, hspD and dsn were analysed using semiquantitative RT-PCR.

RESULTS

We report that the D. discoideum cells displayed PARP activation within 2 min of UV-C irradiation and there was increase in NO levels in a dose-dependent manner. UV-C-irradiated cells had impaired growth, delayed or blocked development and delayed germination compared to control cells. In our previous studies we have shown that inhibition of PARP recovered oxidative stress-induced changes in D. discoideum; however, intriguingly PARP inhibition did not correct all defects as effectively in UV-C-irradiated cells. This possibly was due to interplay with increased NO signalling.

CONCLUSIONS

Our results signify that UV-C and oxidative stress affected growth and development in D. discoideum by different mechanisms; these studies could provide major clues to complex mechanisms of growth and development in higher organisms.

Transcriptomic seasonal variations in a natural population of zebra mussel (Dreissena polymorpha)

The zebra mussel Dreissena polymorpha is a Caspian Sea bivalve that colonized freshwater bodies worldwide during the XX century. To analyze the impact of seasonal and environmental variations on the physiology and metabolism of this invasive species, we developed a custom microarray using 4057 publicly available DNA sequences from Dreissena and other related genera. Transcriptome profiles were analyzed using half-body samples from a relatively clean site (Riba-Roja, low Ebro River, N.E. Spain), at three different stages of the annual cycle: Pre-spawning (February), spawning (June), and gonad resorption (September). Transcripts from a total of 745 unique sequences showed significant changes among these three groups of samples. Functional characterization of these transcripts based on their closest known homologues showed that genes involved in stress defense (oxidative and infection) were overrepresented in September, whereas genes related to reproductive functions were overrepresented in the spawning and pre-spawning periods. This transcriptomic information can help to identify developmental stages at which the organism is more vulnerable for future control strategies. These data will also contribute to the implementation of gene expression-based assays for pollution monitoring in water bodies harboring stable zebra mussel populations.

Regulation of aggregate size and pattern by adenosine and caffeine in cellular slime molds

BACKGROUND

Multicellularity in cellular slime molds is achieved by aggregation of several hundreds to thousands of cells. In the model slime mold Dictyostelium discoideum, adenosine is known to increase the aggregate size and its antagonist caffeine reduces the aggregate size. However, it is not clear if the actions of adenosine and caffeine are evolutionarily conserved among other slime molds known to use structurally unrelated chemoattractants. We have examined how the known factors affecting aggregate size are modulated by adenosine and caffeine.

RESULT

Adenosine and caffeine induced the formation of large and small aggregates respectively, in evolutionarily distinct slime molds known to use diverse chemoattractants for their aggregation. Due to its genetic tractability, we chose D. discoideum to further investigate the factors affecting aggregate size. The changes in aggregate size are caused by the effect of the compounds on several parameters such as cell number and size, cell-cell adhesion, cAMP signal relay and cell counting mechanisms. While some of the effects of these two compounds are opposite to each other, interestingly, both compounds increase the intracellular glucose level and strengthen cell-cell adhesion. These compounds also inhibit the synthesis of cAMP phosphodiesterase (PdsA), weakening the relay of extracellular cAMP signal. Adenosine as well as caffeine rescue mutants impaired in stream formation (pde4- and pdiA-) and colony size (smlA- and ctnA-) and restore their parental aggregate size.

CONCLUSION

Adenosine increased the cell division timings thereby making large number of cells available for aggregation and also it marginally increased the cell size contributing to large aggregate size. Reduced cell division rates and decreased cell size in the presence of caffeine makes the aggregates smaller than controls. Both the compounds altered the speed of the chemotactic amoebae causing a variation in aggregate size. Our data strongly suggests that cytosolic glucose and extracellular cAMP levels are the other major determinants regulating aggregate size and pattern. Importantly, the aggregation process is conserved among different lineages of cellular slime molds despite using unrelated signalling molecules for aggregation.

Autonomous and non-autonomous traits mediate social cooperation in Dictyostelium discoideum

In the trishanku (triA-) mutant of the social amoeba Dictyostelium discoideum, aggregates are smaller than usual and the spore mass is located mid-way up the stalk, not at the apex. We have monitored aggregate territory size, spore allocation and fruiting body morphology in chimaeric groups of (quasi-wild-type) Ax2 and triA- cells. Developmental canalisation breaks down in chimaeras and leads to an increase in phenotypic variation. A minority of triA- cells causes largely Ax2 aggregation streams to break up; the effect is not due to the counting factor. Most chimaeric fruiting bodies resemble those of Ax2 or triA-. Others are double-deckers with a single stalk and two spore masses, one each at the terminus and midway along the stalk. The relative number of spores belonging to the two genotypes depends both on the mixing ratio and on the fruiting body morphology. In double-deckers formed from 1:1 chimaeras, the upper spore mass has more Ax2 spores, and the lower spore mass more triA- spores, than expected. Thus, the traits under study depend partly on the cells' own genotype and partly on the phenotypes, and so genotypes, of other cells: they are both autonomous and non-autonomous. These findings strengthen the parallels between multicellular development and behaviour in social groups. Besides that, they reinforce the point that a trait can be associated with a genotype only in a specified context.

Combining experiments and modelling to understand size regulation in Dictyostelium discoideum

Little is known about how the sizes of specific organs and tissues are regulated. To try to understand these mechanisms, we have been using a combination of modelling and experiments to study the simple system Dictyostelium discoideum, which forms approximately 20000 cell groups. We found that cells secrete a factor, and as the number of cells increases, the concentration of the factor increases. Diffusion calculations indicated that this lets cells sense the local cell density. Computer simulations predicted, and experiments then showed, that this factor decreases cell-cell adhesion and increases random cell motility. In a group, adhesion forces keep cells together, while random motility forces cause cells to pull apart and separate from each other. As the group size increases above a threshold, the factor concentration goes above a threshold and the cells switch from an adhered state to a separated state. This causes excessively large groups to break apart and/or dissipate, creating an upper limit to group size. In this review, we focus on how computer simulations made testable predictions that led the way to understanding the size regulation mechanism mediated by this factor.

A cysteine-rich extracellular protein containing a PA14 domain mediates quorum sensing in Dictyostelium discoideum

Much remains to be understood about quorum-sensing factors that allow cells to sense their local density. Dictyostelium discoideum is a simple eukaryote that grows as single-celled amoebae and switches to multicellular development when food becomes limited. As the growing cells reach a high density, they begin expressing discoidin genes. The cells secrete an unknown factor, and at high cell densities the concomitant high levels of the factor induce discoidin expression. We report here the enrichment of discoidin-inducing complex (DIC), an approximately 400-kDa protein complex that induces discoidin expression during growth and development. Two proteins in the DIC preparation, DicA1 and DicB, were identified by sequencing proteolytic digests. DicA1 and DicB were expressed in Escherichia coli and tested for their ability to induce discoidin during growth and development. Recombinant DicB was unable to induce discoidin expression, while recombinant DicA1 was able to induce discoidin expression. This suggests that DicA1 is an active component of DIC and indicates that posttranslational modification is dispensable for activity. DicA1 mRNA is expressed in vegetative and developing cells. The mature secreted form of DicA1 has a molecular mass of 80 kDa and has a 24-amino-acid cysteine-rich repeat that is similar to repeats in Dictyostelium proteins, such as the extracellular matrix protein ecmB/PstA, the prespore cell-inducing factor PSI, and the cyclic AMP phosphodiesterase inhibitor PDI. Together, the data suggest that DicA1 is a component of a secreted quorum-sensing signal regulating discoidin gene expression during Dictyostelium growth and development.

A gene encoding, prespore-cell-inducing factor in Dictyostelium discoideum

Two factors that exist in conditioned medium (CM) of Dictyostelium discoideum induce amoebae to differentiate into prespore cells when they are incubated at a very low cell density in submerged monolayer culture. Previously, we purified one of them, a glycoprotein factor with an apparent molecular mass of 106 kDa, and we named it psi factor (psi, prespore-inducing factor). Based on the partial amino acid sequence of the purified psi factor, we have isolated the corresponding cDNA clone, which is expressed maximally at the loose mound stage. The cDNA encodes a novel protein and the predicted molecular mass of the mature secreted protein is 60 kDa. Knockout mutant strains of the psi factor gene, psiA(-), were created by targeted integration. Although these mutant strains appear to develop normally, CM from these mutants showed reduced prespore-cell-inducing activity. Rescuing the mutant strains by expression of psi factor under control of a constitutive promoter causes overproduction of psi factor protein and CM from such cells showed a 20-fold higher level of prespore-cell-inducing activity than that from wild-type cells. Further, CM from parental cells induced prespore cell division, while that from psiA null strains showed no cell division inducing activity. Our results indicate that psi factor protein is a novel type of growth factor that does not belong to any of the families of growth factor so far identified in animals.

A cAMP receptor-like G protein-coupled receptor with roles in growth regulation and development

Dictyostelium discoideum uses G protein-mediated signal transduction for many vegetative and developmental functions, suggesting the existence of G protein-coupled receptors (GPCRs) other than the four known cyclic adenosine monophosphate (cAMP) receptors (cAR1-4). Sequences of the cAMP receptors were used to identify Dictyostelium genes encoding cAMP receptor-like proteins, CrlA-C. Limited sequence identity between these putative GPCRs and the cAMP receptors suggests the Crl receptors are unlikely to be receptors for cAMP. The crl genes are expressed at various times during growth and the developmental life cycle. Disruption of individual crl genes did not impair chemotactic responses to folic acid or cAMP or alter cAMP-dependent aggregation. However, crlA(-) mutants grew to a higher cell density than did wild-type cells and high-copy-number crlA expression vectors were detrimental to cell viability, suggesting that CrlA is a negative regulator of cell growth. In addition, crlA(-) mutants produce large aggregates with delayed anterior tip formation indicating a role for the CrlA receptor in the development of the anterior prestalk cell region. The scarcity of GFP-expressing crlA(-) mutants in the anterior prestalk cell region of chimeric organisms supports a cell-autonomous role for the CrlA receptor in prestalk cell differentiation.

Cell motility mediates tissue size regulation in Dictyostelium

Little is known about how organisms regulate the size of multicellular structures. This review condenses some of the observations about how Dictyostelium regulates the size of fruiting bodies. Very large fruiting bodies tend to fall over, and one of the ways Dictyostelium cells prevent this is by breaking up the aggregation streams when there is an excessive number of cells in the stream. Developing cells simultaneously secrete and sense counting factor (CF), a 450 kDa complex of proteins. Diffusion calculations showed that as the number of cells in a stream or group increases, the local concentration of CF will increase, allowing the cells to sense the number of cells in the stream or group. Computer simulations predicted that a high level of CF could trigger stream breakup by decreasing cell-cell adhesion and/or increasing cell motility, effectively causing the stream to dissipate and begin to fall apart. The prediction that adhesion and motility affect group size is supported by observations that decreasing adhesion by adding antibodies that bind to adhesion protein causes the formation of smaller groups, while increasing adhesion by overexpressing adhesion proteins, or decreasing motility with drugs that disrupt actin function both cause the formation of larger groups. CF both decreases adhesion and increases motility. CF increases motility in part by increasing actin polymerization and myosin phosphorylation, and decreasing myosin polymerization. New observations using a fusion of a green fluorescent protein to a protein fragment that binds polymerized actin show that in live cells CF does not affect the distribution of polymerized actin. CF increases the levels of ABP-120, an actin-bundling protein, and new observations indicate that very low levels of CF cause an increase in levels of myoB, an unconventional myosin. Our current understanding of group size regulation in Dictyostelium is thus that motility plays a key role, and that to regulate group size cells regulate the expression of at least two proteins, as well as regulating the polymerization of both actin and myosin.

IfkA, a presumptive eIF2 alpha kinase of Dictyostelium, is required for proper timing of aggregation and regulation of mound size

BACKGROUND

The transition from growth to development in Dictyostelium is initiated by amino acid starvation of growing amobae. In other eukaryotes, a key sensor of amino acid starvation and mediator of the resulting physiological responses is the GCN2 protein, an eIF2alpha kinase. GCN2 downregulates the initiation of translation of bulk mRNA and enhances translation of specific mRNAs by phosphorylating the translation initiation factor eIF2alpha. Two eIF2alpha kinases were identified in Dictyostelium and studied herein.

RESULTS

Neither of the eIF2alpha kinases appeared to be involved in sensing amino acid starvation to initiate development. However, one of the kinases, IfkA, was shown to phosphorylate eIF2alpha from 1 to 7 hours after the onset of development, resulting in a shift from polysomes to free ribosomes for bulk mRNA. In the absence of the eIF2alpha phosphorylation, ifkA null cells aggregated earlier than normal and formed mounds and ultimately fruiting bodies that were larger than normal. The early aggregation phenotype in ifkA null cells reflected an apparent, earlier than normal establishment of the cAMP pulsing system. The large mound phenotype resulted from a reduced extracellular level of Countin, a component of the counting factor that regulates mound size. In wild type cells, phosphorylation of eIF2alpha by IfkA resulted in a specific stabilization and enhanced translational efficiency of countin mRNA even though reduced translation resulted for bulk mRNA.

CONCLUSIONS

IfkA is an eIF2alpha kinase of Dictyostelium that normally phosphorylates eIF2alpha from 1 to 7 hours after the onset of development, or during the preaggregation phase. This results in an overall reduction in the initiation of protein synthesis during this time frame and a concomitant reduction in the number of ribosomes associated with most mRNAs. For some mRNAs, however, initiation of protein synthesis is enhanced or stabilized under the conditions of increased eIF2alpha phosphorylation. This includes countin mRNA.

Cells respond to and bind countin, a component of a multisubunit cell number counting factor

In Dictyostelium discoideum counting factor (CF), a secreted approximately 450-kDa complex of polypeptides, inhibits group and fruiting body size. When the gene encoding countin (a component of CF) was disrupted, cells formed large groups. We find that recombinant countin causes developing cells to form small groups, with an EC(50) of approximately 3 ng/ml, and affects cAMP signal transduction in the same manner as semipurified CF. Recombinant countin increases cell motility, decreases cell-cell adhesion, and regulates gene expression in a manner similar to the effect of CF. However, countin does not decrease adhesion or group size to the extent that semipurified CF does. A 1-min exposure of developing cells to countin causes an increase in F-actin polymerization and myosin phosphorylation and a decrease in myosin polymerization, suggesting that countin activates a rapid signal transduction pathway. (125)I-Labeled countin has countin bioactivity, and binding experiments suggest that vegetative and developing cells have approximately 53 cell-surface sites that bind countin with a K(D) of approximately 1.5 ng/ml or 60 pm. We hypothesize that countin regulates cell development through the same pathway as CF and that other proteins within the complex may modify the activity of countin and/or have independent size-regulating activities.

The different components of a multisubunit cell number-counting factor have both unique and overlapping functions

Dictyostelium aggregation streams break up into groups of 103 to 2×104 cells. The cells sense the number of cells in a stream or group by the level of a secreted counting factor (CF). CF is a complex of at least 5 polypeptides. When the gene encoding countin (one of the CF polypeptides) was disrupted, the cells could not sense each other’s presence, resulting in non-breaking streams that coalesced into abnormally large groups. To understand the function of the components of CF, we have isolated cDNA sequences encoding a second component of CF, CF50. CF50 is 30% identical to lysozyme (but has very little lysozyme activity) and contains distinctive serine-glycine motifs. Transformants with a disrupted cf50 gene, like countin– cells, form abnormally large groups. Addition of recombinant CF50 protein to developing cf50– cells rescues their phenotype by decreasing group size. Abnormalities seen in aggregating countin– cells (such as high cell-cell adhesion and low motility) are also observed in the cf50– cells. Western blot analysis of conditioned medium sieve column fractions showed that the CF50 protein is present in the same fraction as the 450 kDa CF complex. In the absence of CF50, secreted countin is degraded, suggesting that one function of CF50 may be to protect countin from degradation. However, unlike countin– cells, cf50– cells differentiate into an abnormally high percentage of cells expressing SP70 (a marker expressed in a subset of prespore cells), and this difference can be rescued by exposing cells to recombinant CF50. These observations indicate that unlike other known multisubunit factors, CF contains subunits with both overlapping and unique properties.