Structural roles of the spore coat proteins in Dictyostelium discoideum

The integrity of spores formed by mutant strains of Dictyostelium discoideum lacking the major spore coat proteins, SP96, SP70, or SP60, was compared to that of wild-type strains. Single, double, and triple knock-out strains developed normally and produced spores which were indistinguishable from wild-type spores by light or electron microscopy. However, the mutant strains were susceptable to staining with the lectin, ricin A, which recognizes a galactose-rich polysaccharide that is normally hidden by overlying spore coat proteins. The intensity of staining with fluorescently labeled ricinA increased as the spore coat proteins were incrementally lost. While these results indicate that the major outer spore coat proteins are not essential for the construction of a multi-layered spore coat in Dictyostelium, they show that the spores are more porous which might make them at risk to predators before germination.

REMI-RFLP mapping in the Dictyostelium genome

A set of 147 Dictyostelium discoideum strains was constructed by random integration of a vector containing rare restriction sites. The strains were generated by transformation using restriction enzyme-mediated integration (REMI) which results in the integration of linear DNA fragments into randomly distributed genomic restriction sites. Restriction fragment length polymorphism (RFLP) was generated in a single genomic site in each strain. These REMI-RFLP strains were used to confirm gene linkages previously supported by two other physical mapping techniques: yeast artificial chromosome (YAC) contig construction, and megabase-scale restriction mapping. New linkages were uncovered when two or more hybridization probes identified the same RFLP fragments. Probes for 100 genes have marked 53% of the RFLPs, representing greater than 22 Mb of the 40 Mb Dictyostelium genome. Alignment of these and other large fragments along each chromosome should lead to a complete physical map of the Dictyostelium genome.

Progression of an inductive signal activates sporulation in Dictyostelium discoideum

spiA, a marker for sporulation, is expressed during the culmination stage of Dictyostelium development, when the mass of prespore cells has moved partly up the newly formed stalk. Strains containing a full-length spiA promoter/lacZ fusion were stained for beta-galactosidase activity at intervals during development. The results indicate that expression of spiA initiates in prespore cells at the prestalk/prespore boundary (near the apex) and extends downward into the prespore mass as culmination continues. A spatial gradient of staining expands from the top of the prespore mass and intensifies until the front of activation reaches the bottom, whereupon the entire region stains darkly. The spiA promoter can be deleted to within 301 bp of the transcriptional start site with no effect on the relative strength, timing or spatial localization of expression. Further 5′ deletions from −301 to −175 reduce promoter strength incrementally, although timing and spatial expression are not affected. Deletions to −159 and beyond result in inactive promoters. Treatment of early developmental structures with 8-Br-cAMP in situ activates the intracellular cAMP-dependent protein kinase (PKA) and precociously induces spiA expression and sporulation. The absence of an apparent gradient of staining in these structures suggest that PKA is equivalently activatable throughout the prespore region and that all prespore cells are competent to express spiA. Thus, we postulate that the pattern of expression of spiA reveals the progression of an inductive signal for sporulation and suggest that this signal may originate from the prestalk cells at the apex.

Discovery of myosin genes by physical mapping in Dictyostelium

The diversity of the myosin family in a single organism, Dictyostelium discoideum, has been investigated by a strategy devised to rapidly identify and clone additional members of a gene family. An ordered array of yeast artificial chromosome clones that encompasses the Dictyostelium genome was probed at low stringency with conserved regions of the myosin motor domain to identify all possible myosin loci. The previously identified myosin loci (mchA, myoA-E) were detected by hybridization to the probes, as well as an additional seven previously unidentified loci (referred to as myoF-L). Clones corresponding to four of these additional loci (myoF, myoH-J) were obtained by using the isolated yeast artificial chromosomes as templates in a PCR employing degenerate primers specific for conserved regions of the myosin head. Sequence analysis and physical mapping of these clones confirm that these PCR products are derived from four previously unidentified myosin genes. Preliminary analysis of these sequences suggests that at least one of the genes (myoJ) encodes a member of a potentially different class of myosins. With the development of whole genome libraries for a variety of organisms, this approach can be used to rapidly explore the diversity of this and other gene families in a number of systems.

CRAC, a cytosolic protein containing a pleckstrin homology domain, is required for receptor and G protein-mediated activation of adenylyl cyclase in Dictyostelium

Adenylyl cyclase in Dictyostelium, as in higher eukaryotes, is activated through G protein-coupled receptors. Insertional mutagenesis into a gene designated dagA resulted in cells that cannot activate adenylyl cyclase, but have otherwise normal responses to exogenous cAMP. Neither cAMP treatment of intact cells nor GTP gamma S treatment of lysates stimulates adenylyl cyclase activity in dagA mutants. A cytosolic protein that activates adenylyl cyclase, CRAC, has been previously identified. We trace the signaling defect in dagA- cells to the absence of CRAC, and we demonstrate that dagA is the structural gene for CRAC. The 3.2-kb dagA mRNA encodes a predicted 78.5-kD product containing a pleckstrin homology domain, in agreement with the postulated interaction of CRAC with activated G proteins. Although dagA expression is tightly developmentally regulated, the cDNA restores normal development when constitutively expressed in transformed mutant cells. In addition, the megabase region surrounding the dagA locus was mapped. We hypothesize that CRAC acts to connect free G protein beta gamma subunits to adenylyl cyclase activation. If so, it may be the first member of an important class of coupling proteins.

LagC is required for cell-cell interactions that are essential for cell-type differentiation in Dictyostelium

Strain AK127 is a developmental mutant of Dictyostelium discoideum that was isolated by restriction enzyme-mediated integration (REMI). Mutant cells aggregate normally but are unable to proceed past the loose aggregate stage. The cloned gene, lagC (loose aggregate C), encodes a novel protein of 98 kD that contains an amino-terminal signal sequence and a putative carboxy-terminal transmembrane domain. The mutant strain AK127 shows no detectable lagC transcript upon Northern analysis, indicating that the observed phenotype is that of a null allele. Expression of the lagC cDNA in AK127 cells complements the arrest at the loose aggregate stage, indicating that the mutant phenotype results from disruption of the lagC gene. In wild-type cells, lagC mRNA is induced at the loose aggregate stage and is expressed through the remainder of development. lagC- null cells aggregate but then disaggregate and reaggregate to form small granular mounds. Mature spores are produced at an extremely low efficiency (< 0.1% of wild type), appearing only after approximately 72 hr, whereas wild-type strains produce mature spores by 26 hr. lagC- null cells accumulate reduced levels of transcripts for the prestalk-enriched genes rasD and CP2 and do not express the DIF-induced prestalk-specific gene ecmA or the cAMP-induced prespore-specific gene SP60 to significant levels. In chimeric organisms resulting from the coaggregation of lagC- null and wild-type cells, cell-type-specific gene expression is rescued in the lagC- null cells; however, lagC- prespore cells are localized to the posterior of the prespore region and do not form mature spores, suggesting that LagC protein has both no cell-autonomous and cell-autonomous functions. Overexpression of lagC from an actin promoter in both wild-type and lagC- cells causes a delay at the tight aggregate stage, the first stage requiring LagC activity. These results suggest that the LagC protein functions as a nondiffusible cell-cell signaling molecule that is required for multicellular development.

Cell type regulation in response to expression of ricin A in Dictyostelium

Expression of ricin A in either prespore or prestalk cells of Dictyostelium discoideum results in cell-autonomous lethality. Strains expressing the toxic gene under the control of a prestalk-specific regulatory region fail to culminate or form stalks, but form spores normally. Strains expressing ricin A under the control of a prespore-specific regulatory region form neither spores nor stalks. Regulation of the cell types results in conversion of prestalk cells to prespore cells when the prespore cells are poisoned. The newly converted cells then express ricin A and die. In contrast, we could not detect any significant conversion of prespore cells to prestalk cells when the prestalk cells are poisoned under our experimental conditions. This regulation of cell types suggests that the tendency of prestalk cells to regulate and become prespore cells is inhibited by the already established prespore cells. It appears that prespore cells control prestalk cell regulation by producing an inhibitor of prespore differentiation to which they themselves are insensitive.

Enhancer regions responsible for temporal and cell-type-specific expression of a spore coat gene in Dictyostelium

The extracellular spore coat of Dictyostelium discoideum is composed of three major proteins, SP96, SP70, and SP60, encoded by the cotA, cotB, and cotC genes, respectively. The spore coat proteins are coordinately synthesized in prespore cells shortly after aggregation, stored in prespore vesicles during the slug stage, and secreted during encapsulation of spores. We have ligated various portions of the upstream region of cotB to lacZ such that a protein consisting of the first nine amino acids of SP70 fused to beta-galactosidase is synthesized in prespore cells. Individual cells that accumulate the enzyme can be observed in situ during early aggregation due to the sensitivity of the assay. We have found that prespore cells first appear in a random distribution throughout the aggregates with no indication of spatial localization. They subsequently sort out from prestalk cells that form a tip on the aggregates. The cotB regulatory region was subdivided into a proximal and a distal region, each of which could independently direct proper temporal and cell-type control. Transcriptional activity directed by these two regions appears to be additive in the full-length regulatory region. The proximal region was shown to be complex in that removal of certain portions partially reduced transcriptional activity while removal of other portions abolished all activity. Nevertheless, cells transformed with constructs showing attenuated activity expressed the fusion gene at the proper time in development and the activity was localized to prespore cells. The cis-acting regions responsible for all aspects of cotB regulation appear to be closely opposed within the minimal essential sequence of the proximal region.

Tagging developmental genes in Dictyostelium by restriction enzyme-mediated integration of plasmid DNA

Introduction of restriction enzyme along with linearized plasmid results in integration of plasmid DNA at genomic restriction sites in a high proportion of the resulting transformants. We have found that electroporating BamHI or EcoRI together with pyr5-6 plasmids cut with the same enzyme stimulates the efficiency of transformation in Dictyostelium discoideum more than 20-fold over the rate seen when plasmid DNA alone is introduced. Restriction enzyme-mediated integration generates insertions into genomic restriction sites in an apparently random manner, some of which cause mutations. About 1 in 400 of the Dictyostelium transformants displayed arrested or aberrant development. The integrated plasmid, along with flanking genomic DNA, was excised from some of these mutants, cloned in Escherichia coli, and used to transform other Dictyostelium cells. Homologous recombination within the flanking sequences resulted in the same phenotypes displayed by the original mutants, directly demonstrating that the affected genes were responsible for the specific morphological phenotypes. This method of insertional mutagenesis should be useful for tagging, and subsequent cloning, of many developmentally important genes that can be identified by their mutant phenotypes.

Disruption of the sporulation-specific gene spiA in Dictyostelium discoideum leads to spore instability

The spiA gene of Dictyostelium is expressed specifically in prespore cells and spores during culmination, the final stage of development during which prespore and prestalk cells undergo terminal differentiation to form spores and stalk. We have used homologous recombination to delete this gene and have characterized the resulting phenotype. The spiA- strains develop normally and produce spores that are indistinguishable from those of wild-type strains by transmission and scanning electron microscopy. Mutant spores have normal viability when assayed soon after the completion of development, but, as the spiA- spores age, they lose viability more rapidly than those of the spiA+ parent. The drop in viability is more pronounced when spores are submerged in dilute buffer at a concentration that does not allow germination; after 11 days submerged, the viability of spiA- spores is 10(5)-fold reduced, whereas that of the parent is decreased only 10-fold. Reinserting an intact copy of the spiA gene into a spiA- strain restores the stability of its spores. The product of the spiA gene, Dd31, was identified on Western blots as a 30-kD protein using an antibody raised against a fusion protein containing a portion of the coding sequence. Dd31 is associated with the inner face of spore coat fragments in a detergent-resistant manner. This location is consistent with its observed role in maintaining stability of the spores.

Physical mapping of genes to specific chromosomes in Dictyostelium discoideum

Cloned genes were used to probe a highly redundant library of large cloned fragments of the Dictyostelium discoideum genome carried in yeast artificial chromosomes (YACs). Each gene recognized several independent YAC clones, thereby grouping them into a contig. Individual YACs were arranged within the contig by positioning genes relative to rare restriction sites and the YAC ends. Genes that had been previously assigned to one of the six linkage groups by parasexual genetics were used to establish physically mapped regions on specific chromosomes. Previously unmapped genes were assigned to specific chromosomes when they recognized members of a mapped contig. Linkage was confirmed by congruence of large-scale restriction maps centered on either the previously mapped or the newly mapped genes. At present, the chromosome-assigned map segments comprise approximately 50% of the genome. About half of each map segment is covered by overlapping YACs.

A prespore gene, Dd31, expressed during culmination of Dictyostelium discoideum

During culmination of Dictyostelium fruiting bodies, prespore and prestalk cells undergo terminal differentiation to form spores and a cellular stalk. A genomic fragment was isolated by random cloning that hybridizes to a 1.4-kb mRNA present during culmination. Cell type separations at culmination showed that the mRNA is present in prespore cells and spores, but not in prestalk or stalk cells. After genomic mapping, an additional 3 kb of DNA surrounding the original 1-kb fragment was cloned. The gene was sequenced and named Dd31 after the size of the predicted protein product in kilodaltons. Accumulation of Dd31 mRNA occurs immediately prior to sporulation. Addition of 20 mM 8-Br-cAMP to cells dissociated from Mexican hat stage culminants induced sporulation and the accumulation of Dd31 mRNA, while 20 mM cAMP did not. Dd31 mRNA does not accumulate in the homeotic mutant stalky in which prespore cells are converted to stalk cells rather than spores. Characterization of Dd31 extends the known temporal dependent sequence of molecular differentiations to sporulation.

Coordinate regulation of the spore coat genes in Dictyostelium discoideum

Genomic clones of the genes coding for the three major spore coat proteins, SP60, SP70, and SP96, were used to measure the accumulation of their respective mRNAs in mutant and wild-type cells allowed to develop under a variety of conditions. These prespore-specific mRNAs were found to be both temporally and quantitatively coordinate under all conditions indicating that they may be subject to identical regulatory processes. Accumulation of the spore coat mRNAs is dependent upon the function of both cAMP receptors and G alpha 2 proteins during the aggregation stage as well as upon concomitant protein synthesis. When cells are dissociated from aggregates at 10 hr of development and rapidly shaken in 0.1 mM EDTA they form clumps but do not accumulate any of the prespore-specific RNAs assayed. However, if either 0.1 mM Ca++ or 20 microM cAMP is added to these cells, the spore coat mRNAs accumulate. Lower concentrations of either Ca++ or cAMP had no effect. These results suggest that expression of the spore coat genes normally involves a Ca+(+)-dependent process, but the Ca++ requirement can be overcome by adding high concentrations of exogenous cAMP. Addition of 50 nM DIF to dissociated cell blocks the accumulation of the spore coat mRNAs even when cAMP or Ca++ is present. The upstream regions of the spore coat genes were compared to those of another gene, D19, that codes for the prespore-specific protein SP29. Short sequences related to CACCCAC were found at about the same position relative to the transcriptional start sites of these coordinately regulated genes.

Molecular phylogeny of Dictyostelium discoideum by protein sequence comparison

Comparison of the amino acid sequences of eight proteins from the soil amoeba Dictyostelium discoideum to those of their homologs in bacteria, yeast, and other eukaryotes indicates that Dictyostelium diverged from the line leading to mammals at about the same time as the plant/animal divergence. Yeast appear to have diverged considerably earlier. It is argued that previous analyses indicating that D. discoideum diverged before yeast were misleading because of the nature of the small ribosomal subunit rRNA sequences used in these studies. We suggest that amino acid sequences may be more reliable than untranslated nucleic acid sequences for evolutionary comparisons, especially among organisms with significant skewing of their A+T content.

Cell-free N-glycosylation in Dictyostelium discoideum: analysis of wild-type and mutants defective in lipid-linked oligosaccharide biosynthesis

N-glycosylation was measured in wild-type cell lysates of Dictyostelium discoideum and in two mutant strains that synthesize a truncated lipid-linked oligosaccharide, Man6GlcNAc2 lacking terminal mannose and glucose residues. Endogenous lipid-linked oligosaccharide (LLO) was transferred to octanoyl-Asn-[125I]Tyr-ThrNH2 by membrane fractions. About 50% of the glycopeptide product remained associated with membranes. Taurocholate and saponin promoted and preserved glycosylation, but NP-40 and Triton X-100 did not. Using this artificial assay, the rate and extent of transfer of the truncated lipid-linked oligosaccharide in extracts of the two mutant strains, HL241 and HL243, was reduced 5-10-fold relative to that of wild-type. The low activity found in the mutant strains appears to result from either reduced affinity of the truncated LLO for the transferase or from its improper topological localization in the membrane. When protein N-glycosylation is measured in living cells it is nearly normal in HL241, but it is 3-4-fold decreased in HL243. Although the results of the in vitro and in vivo assays differ, they are not in conflict. Rather, they suggest that the static in vitro assay may be capable of revealing subtleties in the productive positioning of LLO and the oligosaccharyl transferase. The decrease in glycosylation seen in intact HL243 cells may be a consequence of the pleiotropic effects of the primary mutation rather than a direct result of the altered LLO structure. Genetic analysis showed that the mutation in HL241 is recessive, while the mutation in HL243 is dominant and prevents normal development. Thus, the two mutants share a lesion in lipid-linked oligosaccharide biosynthesis and in cell-free glycosylation, but differ in their in vivo glycosylation. Their primary defects are probably different.

A pair of tandemly repeated genes code for gp24, a putative adhesion protein of Dictyostelium discoideum

The glycoprotein gp24 has been implicated in cell-cell adhesion of Dictyostelium discoideum. We have used a cDNA clone that codes for gp24 to screen cloned genomic fragments. Two closely linked genes (GP24A and GP24B) were recognized that generate mRNAs of about 650 base pairs after excision of a small intron and addition of poly(A). They appear to have arisen by tandem duplication of about 800 base pairs, followed by divergence. These genes are expressed within a few hours of the initiation of development; their mRNAs accumulate to a peak at 12 hr and persist until culmination. Both genes have short guanine-rich sequences (G boxes) upstream that have been shown to be involved in transcriptional regulation of other genes expressed during development of Dictyostelium. Their mRNAs code for proteins that are 85% identical. GP24A and GP24B mRNAs code for proteins with a hydrophobic domain followed by a highly charged carboxyl-terminal domain.

Similarities in eukaryotic genomes

1. The degree of overlap between the human genome and that of other eukaryotes is considered. Biochemical and molecular studies have shown that all eukaryotic organisms evolved from a common progenator that lived several billion years ago. 2. From a geneological point of view, all eukaryotes are related and their genes are all descended from common ancestors. 3. However, most of the DNA in eukaryotic genomes is not transcribed and has been free to drift in nucleotide sequence. Therefore, the question of overlap can only be applied meaningfully to the few per cent of the genome that is expressed. 4. During the last billion years many genes have duplicated and diverged and new genes have been formed by accretion of domains copied from other genes (exon shuffling). 5. The rate of genetic divergence has been such that only a few portions coding for pieces of highly conserved proteins are still shared by all eukaryotes including those that diverged over 600 million years ago. 6. On the other hand, a fairly large number of shared genes can be recognized among species that separated within the last few hundred million years. 7. Human genes have a high degree of identity with homologs in closely related organisms such as other mammals and a decreasing level of identity with their homologs in more distantly related species.

Spore coat genes SP60 and SP70 of Dictyostelium discoideum

We cloned and sequenced the genes for two of the major proteins found in spore coats of Dictyostelium discoideum. The predicted translation product of each of these genes starts with a hydrophobic signal sequence that is subsequently cleaved. Expression of these spore coat genes is coordinate in prespore cells.

Developmental consequences of the lack of myosin heavy chain in Dictyostelium discoideum

Two different Dictyostelium discoideum cell lines that lack myosin heavy chain protein (MHC A) have been previously described. One cell line (mhcA) was created by antisense RNA inactivation of the endogenous mRNA and the other (HMM) by insertional mutagenesis of the endogenous myosin gene. The two cell lines show similar developmental defects; they are delayed in aggregation and become arrested at the mound stage. However, when cells that lack myosin heavy chain are mixed with wild-type cells, some of the mutant cells are capable of completing development to form mature spores. The pattern of expression of a number of developmentally regulated genes has been examined in both mutant cell lines. Although morphogenesis becomes aberrant before aggregation is completed, all of the markers that we have examined are expressed normally. These include genes expressed prior to aggregation as well as prespore genes expressed later in development. It appears that the signals necessary for cell-type differentiation are generated in the aborted structures formed by cells lacking MHC A. The mhcA cells have negligible amounts of MHC A protein while the HMM cells express normal amounts of a fragment of the myosin heavy chain protein similar to heavy meromyosin (HMM). The expression of myosin light chain was examined in these two cell lines. HMM cells accumulate normal amounts of the 18,000-D light chain, while the amount of light chain in mhcA cells is dramatically reduced. It is likely that the light chains assemble normally with the HMM fragment in HMM cells, while in cells lacking myosin heavy chain (mhcA) the light chains are unstable.

Cell motility and chemotaxis in Dictyostelium amebae lacking myosin heavy chain

Dictyostelium amebae have been engineered by homologous recombination of a truncated copy of the myosin heavy chain gene (heavy meromyosin (HMM) cells) and by transformation with a vector encoding an antisense RNA to myosin heavy chain mRNA (mhcA cells) so that they lack native myosin heavy chain protein. In the former case, cells synthesize only the heavy meromyosin portion of the protein and in the latter case they synthesize negligible amounts of the protein. Surprisingly, it was demonstrated that both cell lines are viable and motile. In order to compare the motility of these cells with normal cells, the newly developed computer-assisted Dynamic Morphology System (DMS) was employed. The results demonstrate that the average HMM or mhcA ameba moves at a rate of translocation less than half that of normal cells. It is rounder and less polar than a normal cell, and exhibits a rate of cytoplasmic expansion and contraction roughly half that of normal cells. In a spatial gradient of cAMP, the average ameba of HMM or mhcA exhibits a chemotactic index of +0.10 or less, compared to the chemotactic index of +0.50 exhibited by normal cells. Finally, the initial area, rate of expansion, and final area of pseudopods are roughly half that of normal cells. The five fastest HMM amebae (out of 35 analyzed in detail) moved at an average rate of translocation equal to that of normal amebae, and exhibited an average chemotactic index of +0.34. In addition, the average rate of cytoplasmic flow in fast HMM cells was equal to that of the average normal ameba. However, fast HMM amebae still exhibited the same defects in pseudopod formation that were exhibited by the entire HMM cell population. These results suggest that myosin heavy chain is involved in the "fine tuning" and efficiency of pseudopod formation, but is not essential for the basic behavior of pseudopod expansion.

Signal transduction, chemotaxis, and cell aggregation in Dictyostelium discoideum cells without myosin heavy chain

Dictyostelium discoideum cells have been generated that lack myosin heavy chain (MHC) due to antisense RNA inactivation of the endogenous mRNA or to insertional mutagenesis of the myosin gene. These cells retain chemotactic movement in gradients of the chemoattractant cAMP. Furthermore, cAMP does induce many biochemical and physiological responses in aggregative cells, including binding of cAMP to surface receptors, modification, and down-regulation of the receptor; activation of adenylate and guanylate cyclase, secretion of cAMP; and the association of actin to the Triton-insoluble cytoskeleton. Cells lacking MHC were found to have a requirement for bivalent cations in the medium for optimal chemotaxis and cell aggregation.

Regulation of SP60 mRNA during development of Dictyostelium discoideum

The accumulation of mRNA recognized by oligonucleotides coding for a portion of the spore coat protein, SP60, was determined throughout development of Dictyostelium discoideum. The 1.8 kb mRNA first appears at the tipped aggregate stage and accumulates until culmination. This mRNA is present in pre-spore cells but absent from pre-stalk cells. A cDNA clone was selected by the oligonucleotides and found to be homologous to this mRNA. Although the oligonucleotides were designed to match the sequence coding for a hexapeptide repeat at the amino-terminus of SP60, they were able to recognize a similar repeated region at the carboxy-terminus of the protein coded by the cDNA clone. The SP60 gene appears to be subject to temporal and cell-type-specific transcriptional controls that are coordinate with those of SP96, another spore coat gene.