REMI-RFLP mapping in the Dictyostelium genome

Molecular pharmacology in a simple model system: implicating MAP kinase and phosphoinositide signalling in bipolar disorder

Understanding the mechanisms of drug action has been the primary focus for pharmacological researchers, traditionally using rodent models. However, non-sentient model systems are now increasingly being used as an alternative approach to better understand drug action or targets. One of these model systems, the social amoeba Dictyostelium, enables the rapid ablation or over-expression of genes, and the subsequent use of isogenic cell culture for the analysis of cell signalling pathways in pharmacological research. The model also supports an increasingly important ethical view of research, involving the reduction, replacement and refinement of animals in biomedical research. This review outlines the use of Dictyostelium in understanding the pharmacological action of two commonly used bipolar disorder treatments (valproic acid and lithium). Both of these compounds regulate mitogen activated protein (MAP) kinase and inositol phospholipid-based signalling by unknown means. Analysis of the molecular pathways targeted by these drugs in Dictyostelium and translation of discoveries to animal systems has helped to further understand the molecular mechanisms of these bipolar disorder treatments.

Dictyostelium discoideum CenB is a bona fide centrin essential for nuclear architecture and centrosome stability

Centrins are a family of proteins within the calcium-binding EF-hand superfamily. In addition to their archetypical role at the microtubule organizing center (MTOC), centrins have acquired multiple functionalities throughout the course of evolution. For example, centrins have been linked to different nuclear activities, including mRNA export and DNA repair. Dictyostelium discoideum centrin B is a divergent member of the centrin family. At the amino acid level, DdCenB shows 51% identity with its closest relative and only paralog, DdCenA. Phylogenetic analysis revealed that DdCenB and DdCenA form a well-supported monophyletic and divergent group within the centrin family of proteins. Interestingly, fluorescently tagged versions of DdCenB were not found at the centrosome (in whole cells or in isolated centrosomes). Instead, DdCenB localized to the nuclei of interphase cells. This localization disappeared as the cells entered mitosis, although Dictyostelium cells undergo a closed mitosis in which the nuclear envelope (NE) does not break down. DdCenB knockout cells exhibited aberrant nuclear architecture, characterized by enlarged and deformed nuclei and loss of proper centrosome-nucleus anchoring (observed as NE protrusions). At the centrosome, loss of DdCenB resulted in defects in the organization and morphology of the MTOC and supernumerary centrosomes and centrosome-related bodies. The multiple defects that the loss of DdCenB generated at the centrosome can be explained by its atypical division cycle, transitioning into the NE as it divides at mitosis. On the basis of these findings, we propose that DdCenB is required at interphase to maintain proper nuclear architecture, and before delocalizing from the nucleus, DdCenB is part of the centrosome duplication machinery.

cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum

A pair of adjacent genes, impA and dia1, are divergently transcribed but expressed at different stages in the life cycle of Dictyostelium discoideum. The intervening 654-bp region carries cis-acting regions that are essential for transcription in both directions as well as repression of dia1 in growing cells. We have focused on a 112-bp region proximal to dia1 that is essential for bidirectional transcription. Analyses of a set of internal deletions showed that the sequence between positions 80 and 97 (TTTGAATTTTTTGAATTT) is critical and that bases outside this region are dispensable. Site-directed mutations within this critical region confirmed the importance of this sequence for transcription both to the right and to the left. However, insertions of either 6 or 24 Ts into the run of 6 Ts separating the repeated GAA sequence had little effect on the functioning of the site in either direction, suggesting that factors recognize the half-sites TTGAATT separately. Inversion of the bases between positions 80 and 97 greatly reduced expression in both directions, indicating that orientation is critical for expression of both the nearby impA gene and the distal dia1 gene, which is more than 500 bp away. Comparison of 38 mutant constructs with multiple random variations in the region indicated that transcription factors may bind to a range of related sequences and still retain function. All functional constructs directed transcription both leftward and rightward, while all nonfunctional constructs were impaired for transcription in both directions. It appears that the same transcription complex controls transcription of both impA and dia1.

The Shwachman-Bodian-Diamond syndrome gene encodes an RNA-binding protein that localizes to the pseudopod ofDictyosteliumamoebae during chemotaxis

The Shwachman-Bodian-Diamond syndrome (SBDS) is an autosomal disorder with multisystem defects. The Shwachman-Bodian-Diamond syndrome gene (SBDS), which contains mutations in a majority of SBDS patients, encodes a protein of unknown function, although it has been strongly implicated in RNA metabolism. There is also some evidence that it interacts with molecules that regulate cytoskeletal organization. Recently, it has been demonstrated by computer-assisted methods that the single behavioral defect of polymorphonuclear leukocytes (PMNs) of SBDS patients is the incapacity to orient correctly in a spatial gradient of chemoattractant. We considered using the social amoeba Dictyostelium discoideum, a model for PMN chemotaxis, an excellent system for elucidating the function of the SBDS protein. We first identified the homolog of SBDS in D. discoideum and found that the amino acids that are altered in human disease were conserved. Given that several proteins involved in chemotactic orientation localize to the pseudopods of cells undergoing chemotaxis, we tested whether the SBDS gene product did the same. We produced an SBDS-GFP chimeric in-frame fusion gene, and generated transformants either with multiple ectopic insertions of the fusion gene or multiple copies of a non-integrated plasmid carrying the fusion gene. In both cases, the SBDS-GFP protein was dispersed equally through the cytoplasm and pseudopods of cells migrating in buffer. However, we observed differential enrichment of SBDS in the pseudopods of cells treated with the chemoattractant cAMP, suggesting that the SBDS protein may play a role in chemotaxis. In light of these results, we discuss how SBDS might function during chemotaxis.

A user's guide to restriction enzyme-mediated integration in Dictyostelium

Restriction enzyme-mediated integration (REMI) has been used to study a number of cellular and developmental processes in Dictyostelium discoideum. In this paper we review the basics of this powerful method of introducing random mutations in Dictyostelium. Here we discuss several mutation screens that have been devised and some of the genes that have been discovered through this approach to mutagenesis. Included in this discussion is how one goes about isolating a gene that has been disrupted by REMI, and how one confirms that this disruption is actually responsible for the observed phenotype. Finally, we describe how REMI can be used as an effective teaching tool in undergraduate cell biology laboratory courses.

A second UDP-glucose pyrophosphorylase is required for differentiation and development in Dictyostelium discoideum

Uridine diphosphoglucose pyrophosphorylase (UDPGP) is a developmentally regulated enzyme in Dictyostelium discoideum, which is involved in trehalose, cellulose, and glycogen synthesis. Two independent UDPGP proteins are believed to be responsible for this activity. To determine the relative contributions of each protein, the genes encoding them were disrupted individually. Cells lacking the udpgp1 gene exhibit normal growth and development and make normal levels of cellulose. In agreement with these phenotypes, udpgp1(-) cells still have UDPGP activity, although at a reduced level. This supports the importance of the second UDPGP gene. This newly identified gene, ugpB, encodes an active UDPGP as determined by complementation in Escherichia coli. When this gene is disrupted, cells undergo aberrant differentiation and development ending with small, gnarled fruiting bodies. These cells also have decreased spore viability and decreased levels of glycogen, whose production requires UDPGP activity. These phenotypes suggest that UgpB constitutes the major UDPGP activity produced during development. Sequence analysis of the two UDPGP genes shows that UgpB has higher homology to other eukaryotic UDPGPs than does UDPGP1. This includes the presence of 5 conserved lysine residues. Udpgp1 only has 1 of these lysines.

Ege A, a novel C2 domain containing protein, is essential for GPCR-mediated gene expression in dictyostelium

During early stages of development, expression of aggregative genes in Dictyostelium is regulated by G protein-linked signaling pathways. We have isolated an aggregation-deficient mutant from a restriction enzyme-mediated insertional mutagenesis screen and have obtained its cDNA. Since the mutant expresses prestarvation genes but fails to express early genes, such as cAR1 and GP80, during development, we designated it early gene expression A (ege A). Ege A, encoding a cytosolic protein of 26 kDa, along with Ege B, belongs to a novel C2 domain-containing gene family. While Ege A mRNA is expressed during the first 2 h of development, Ege B is expressed at later stages. Ege A is not directly required for either G protein-mediated actin polymerization or activation of adenylyl cyclase. Ege A overexpressing and ege A(-) cells display similar phenotypes, suggesting that an optimal level of Ege A is required for proper function. Constitutive expression of a fully functional cAR1-YFP enables ege A(-) cells to form loose aggregates, but cAR1-YFP/ege A(-) cells are still unable to express GP80, suggesting that losses of gene expression were not solely due to a lack of cAR1. Overexpression of PKAcat, the constitutively active subunit of PKA, does not rescue the ege A(-) phenotype, suggesting that PKA is not located downstream from Ege A in the signaling pathway. We propose that Ege A is a novel cytosolic component required by early gene expression.

Restriction enzymes increase efficiencies of illegitimate DNA integration but decrease homologous integration in mammalian cells

Mammalian cells repair DNA double-strand breaks by illegitimate end-joining or by homologous recombination. We investigated the effects of restriction enzymes on illegitimate and homologous DNA integration in mammalian cells. A plasmid containing the neo(R) expression cassette, which confers G418 resistance, was used to select for illegitimate integration events in CHO wild-type and xrcc5 mutant cells. Co-transfection with the restriction enzymes BamHI, BglII, EcoRI and KpnI increased the efficiency of linearized plasmid integration up to 5-fold in CHO cells. In contrast, the restriction enzymes did not increase the integration efficiency in xrcc5 mutant cells. Effects of restriction enzymes on illegitimate and homologous integration were also studied in mouse embryonic stem (ES) cells using a plasmid containing the neo(R) gene flanked by exon 3 of HPRT: The enzymes BamHI, BglII and EcoRI increased the illegitimate integration efficiency of transforming DNA several-fold, similar to the results for CHO cells. However, all three enzymes decreased the absolute frequency of homologous integration approximately 2-fold, and the percentage of homologous integration decreased >10-fold. This suggests that random DNA breaks attract illegitimate recombination (IR) events that compete with homology search.

Toward the functional analysis of the Dictyostelium discoideum genome

Dictyostelium discoideum is a useful model for molecular studies of cell biology and development. The 34-megabase Dictyostelium genome is currently being sequenced through the efforts of an international consortium. The genome is expected to encode 8-10,000 genes, including all those required for a free-living eukaryote capable of multicellular development. A complete description of the Dictyostelium genome will open the way toward the application of genome-based experimental approaches to studies of cell biology and development in this organism, and allow detailed physiological and evolutionary comparisons to other species.

The cellulose synthase gene of Dictyostelium

Cellulose is a major component of the extracellular matrices formed during development of the social amoeba, Dictyostelium discoideum. We isolated insertional mutants that failed to accumulate cellulose and had no cellulose synthase activity at any stage of development. Development proceeded normally in the null mutants up to the beginning of stalk formation, at which point the culminating structures collapsed onto themselves, then proceeded to attempt culmination again. No spores or stalk cells were ever made in the mutants, with all cells eventually lysing. The predicted product of the disrupted gene (dcsA) showed significant similarity to the catalytic subunit of cellulose synthases found in bacteria. Enzyme activity and normal development were recovered in strains transformed with a construct expressing the intact dcsA gene. Growing amoebae carrying the construct accumulated the protein product of dcsA, but did not make cellulose until they had developed for at least 10 hr. These studies show directly that the product of dcsA is necessary, but not sufficient, for synthesis of cellulose.

Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae has been the principal organism used in experiments to examine genetic recombination in eukaryotes. Studies over the past decade have shown that meiotic recombination and probably most mitotic recombination arise from the repair of double-strand breaks (DSBs). There are multiple pathways by which such DSBs can be repaired, including several homologous recombination pathways and still other nonhomologous mechanisms. Our understanding has also been greatly enriched by the characterization of many proteins involved in recombination and by insights that link aspects of DNA repair to chromosome replication. New molecular models of DSB-induced gene conversion are presented. This review encompasses these different aspects of DSB-induced recombination in Saccharomyces and attempts to relate genetic, molecular biological, and biochemical studies of the processes of DNA repair and recombination.

Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae has been the principal organism used in experiments to examine genetic recombination in eukaryotes. Studies over the past decade have shown that meiotic recombination and probably most mitotic recombination arise from the repair of double-strand breaks (DSBs). There are multiple pathways by which such DSBs can be repaired, including several homologous recombination pathways and still other nonhomologous mechanisms. Our understanding has also been greatly enriched by the characterization of many proteins involved in recombination and by insights that link aspects of DNA repair to chromosome replication. New molecular models of DSB-induced gene conversion are presented. This review encompasses these different aspects of DSB-induced recombination in Saccharomyces and attempts to relate genetic, molecular biological, and biochemical studies of the processes of DNA repair and recombination.

Genetic analysis in fungi using restriction-enzyme-mediated integration

Restriction-enzyme-mediated integration (REMI), a method for generating nonhomologous integration of transforming DNA into the chromosomes of eukaryotic cells, has been used for insertion mutagenesis and other genetic studies in diverse organisms. Insertion mutations generated by REMI have facilitated the genetic dissection of developmental pathways in Dictyostelium discoidium and the isolation of virulence factors in several plant pathogenic fungi. Recent work indicates that REMI occurs by nonhomologous end joining.

Nonhomologous end joining during restriction enzyme-mediated DNA integration in Saccharomyces cerevisiae

The BamHI restriction enzyme mediates integration of nonhomologous DNA into the Saccharomyces cerevisiae genome (R. H. Schiestl and T. D. Petes, Proc. Natl. Acad. Sci. USA 88:7585-7589, 1991). The present study investigates the mechanism of such events: in particular, the mediating activity of various restriction enzymes and the processing of resultant fragment ends. Our results show that in addition to BamHI, BglII and KpnI increase DNA integration efficiencies severalfold, while Asp718, HindIII, EcoRI, SalI, SmaI, HpaI, MscI, and SnaBI do not. Secondly, the three active enzymes stimulated integrations only of fragments containing 5' or 3' overhangs but not of blunt-ended fragments. Thirdly, integrations mediated by one enzyme and utilizing a substrate created by another required at least 2 bp of homology. Furthermore, an Asp718 fragment possessing a 5' overhang integrated into a KpnI (isoschizomer) site possessing a 3' overhang, most likely by filling of the 5' overhang followed by 5' exonuclease digestion to produce a 3' end. We classified and analyzed the restriction enzyme-mediated integration events in the context of their genomic positions. The majority of events integrated into single sites. In the remaining 6 of 19 cases each end of the plasmid inserted into a different sequence, producing rearrangements such as duplications, deletions, and translocations.

Replicon rescue: a novel strategy to clone the genomic DNA flanking insertions of integrating shuttle vector DNA

A novel cloning strategy, replicon rescue, was developed for cloning genes disrupted by plasmid insertions. After ligation to a tetracycline resistance cassette, fragments containing a bacterial origin of replication from the insertion are recovered in Escherichia coli because they replicate autonomously. Restriction enzymes for cloning are so chosen that the only legitimate two fragment ligation yielding TetR clones involves a fragment spanning the boundary of the insertion. Replicon rescue was used successfully firstly in a test system to clone the chromosomal orl from a Klebsiella aerogenes strain, and secondly to recover a disrupted gene from a phototaxis-deficient mutant of Dictyostelium.

Ordered yeast artificial chromosome clones representing the Dictyostelium discoideum genome

High resolution gene maps of the six chromosomes of Dictyostelium discoideum have been generated by a combination of physical mapping techniques. A set of yeast artificial chromosome clones has been ordered into overlapping arrays that cover >98% of the 34-magabase pair genome. Clones were grouped and ordered according to the genes they carried, as determined by hybridization analyses with DNA fragments from several hundred genes. Congruence of the gene order within each arrangement of clones with the gene order determined from whole genome restriction site mapping indicates that a high degree of confidence can be placed on the clone map. This clone-based description of the Dictyostelium chromosomes should be useful for the physical mapping and subcloning of new genes and should facilitate more detailed analyses of this genome. cost of silicon-based construction and in the efficient sample handling afforded by component integration.

Social senses: G-protein-coupled receptor signaling pathways in Dictyostelium discoideum

Activation of the chemoattractant receptor of Dictyostelium elicits many of the same biochemical events seen when mammalian G-protein-coupled receptors are activated. Studies in this organism provide evidence for new signaling pathways that are activated by receptors of this type, and fresh insights into the mechanism of signal transduction by G proteins.

Analysis of gene function in Dictyostelium

Over the past ten years, powerful molecular genetic techniques have been developed to analyze gene function in Dictyostelium. DNA-mediated transformation using a variety of selections and vectors has allowed the introduction of wild-type or modified genes that are under various forms of transcriptional control. Homologous recombination is efficient and can be used to modify the genome in precise ways. In addition, it is now possible to clone genes based on their mutant phenotype alone, either by insertional mutagenesis, or by screening antisense expression cDNA libraries. Finally, a nearly complete physical map of the genome is available and so genes are easily mapped by physical techniques. We discuss many of these advances within the context of major research problems presently under study.

Integrated maps of the chromosomes in Dictyostelium discoideum

Detailed maps of the six chromosomes that carry the genes of Dictyostelium discoideum were constructed by correlating physically mapped regions with parasexually determined linkage groups. Chromosomally assigned regions were ordered and positioned by the pattern of altered fragment sizes seen in a set of restriction enzyme mediated integration-restriction fragment length polymorphism (REMI-RFLP) strains each harboring an inserted plasmid that carries sites recognized by NotI, SstI, SmaI, BglI and ApaI. These restriction enzymes were used to digest high molecular weight DNA prepared from more than 100 REMI-RFLP strains and the resulting fragments were separated and sized by pulsed-field gels. More than 150 gene probes were hybridized to blots of these gels and used to map the insertion sites relative to flanking restriction sites. In this way, we have been able to restriction map the 35 mb genome as well as determine the map position of more than 150 genes to with approximately 40 kb resolution. These maps provide a framework for subsequent refinement.

A multidrug resistance transporter/serine protease gene is required for prestalk specialization in Dictyostelium

The prestalk-specific gene, tagB, was disrupted by restriction enzyme-mediated integration (REMI) mutagenesis. Mutant aggregates exhibit a cell-autonomous defect in specialization of PST-A cells, a prestalk subpopulation that forms the tip and eventually forms the stalk of the fruiting body. Cooperative (non-cell-autonomous) defects were found in sporulation and in specialization of prestalk cells that eventually form the upper cup of the fruiting body (PST-O). The pattern of ecmA::lacZ expression in mutant tagB- cells defines a primary prestalk population, PST-I, from which other prestalk cells differentiate. After PST-A cells differentiate, they induce remaining PST-I cells to become PST-O cells. Subsequently, prestalk cells induce encapsulation of prespore cells during culmination. tagB is homologous to serine protease and to multidrug resistance (MDR) transporter genes, implying a mechanism of action that includes proteolysis and export of peptide signals. Intercellular communication via TagB may mediate integration of cellular differentiation with morphogenesis.