Phenocopy of discoidin I-minus mutants by antisense transformation in Dictyostelium

Evidence that the StlA polyketide synthase is required for the transition of growth to development in Polysphondylium violaceum

The social amoeba Polysphondylium violaceum uses chemoattractants different from those of Dictyoctelium discoideum for cell aggregation. However, the detailed mechanisms in P. violaceum remain unknown. We have previously reported that the polyketide synthase StlA is involved in inducing aggregation in this species. To elucidate the mechanism of StlA-induced aggregation in P. violaceum, we analyzed the phenotype of P. violaceum stlA- (Pv-stlA-) mutants in more detail. Unlike our previous results, the mutant cells did not exhibit proper chemotaxis toward glorin. Defective aggregation was not restored by glorin pulses, 8Br-cAMP, or deletion of the homologue of PufA that is a translational repressor of protein kinase A, whereas mutant cells grown in the presence of 4-methyl-5-pentylbenzene-1,3-diol (MPBD), the putative Pv-StlA product, aggregated normally without it after starvation. Furthermore, the early developmental marker gene, dscA, was downregulated in the mutant cells. Our data thus suggested that StlA is required for the transition from growth to development in P. violaceum.

Prestalk-like positioning of de-differentiated cells in the social amoeba Dictyostelium discoideum

The social amoeba Dictyostelium discoideum switches between solitary growth and social fruitification depending on nutrient availability. Under starvation, cells aggregate and form fruiting bodies consisting of spores and altruistic stalk cells. Once cells socially committed, they complete fruitification, even if a new source of nutrients becomes available. This social commitment is puzzling because it hinders individual cells from resuming solitary growth quickly. One idea posits that traits that facilitate premature de-commitment are hindered from being selected. We studied outcomes of the premature de-commitment through forced refeeding. Our results show that when refed cells interacted with non-refed cells, some of them became solitary, whereas a fraction was redirected to the altruistic stalk, regardless of their original fate. The refed cells exhibited reduced cohesiveness and were sorted out during morphogenesis. Our findings provide an insight into a division of labor of the social amoeba, in which less cohesive individuals become altruists.

An evolutionarily conserved coronin-dependent pathway defines cell population size

Maintenance of cell population size is fundamental to the proper functioning of multicellular organisms. Here, we describe a cell-intrinsic cell density–sensing pathway that enabled T cells to reach and maintain an appropriate population size. This pathway operated “kin-to-kin” or between identical or similar T cell populations occupying a niche within a tissue or organ, such as the lymph nodes, spleen, and blood. We showed that this pathway depended on the cell density–dependent abundance of the evolutionarily conserved protein coronin 1, which coordinated prosurvival signaling with the inhibition of cell death until the cell population reached threshold densities. At or above threshold densities, coronin 1 expression peaked and remained stable, thereby resulting in the initiation of apoptosis through kin-to-kin intercellular signaling to return the cell population to the appropriate cell density. This cell population size-controlling pathway was conserved from amoeba to humans, thus providing evidence for the existence of a coronin-regulated, evolutionarily conserved mechanism by which cells are informed of and coordinate their relative population size.

An improved shotgun antisense method for mutagenesis and gene identification

Shotgun expression of antisense cDNA, where each transformed cell expresses a different antisense cDNA, has been used for mutagenesis and gene identification in Dictyostelium discoideum. However, the method has two limitations. First, there were too few clones in the shotgun antisense cDNA library to have an antisense cDNA for every gene in the genome. Second, the unequal transcription level of genes resulted in many antisense cDNAs in the library for some genes but relatively few antisense cDNAs for other genes. Here we report an improved method for generating a larger antisense cDNA library with a reduced percentage of cDNA clones from highly prevalent mRNAs and demonstrate its utility by screening for signal transduction pathway components in D. discoideum.

We present an improved shotgun antisense method for generating gene expression knockdown mutants. This method incorporates a cDNA-normalization step to equalize the transcript number of each gene in the antisense cDNA library.

The Use of Diffusion Calculations and Monte Carlo Simulations to Understand the Behavior of Cells in Dictyostelium Communities

Microbial communities are the simplest possible model of multicellular tissues, allowing studies of cell-cell interactions to be done with as few extraneous factors as possible. For instance, the eukaryotic microbe Dictyostelium discoideum proliferates as single cells, and when starved, the cells aggregate together and form structures of ~20,000 cells. The cells use a variety of signals to direct their movement, inform each other of their local cell density and whether they are starving, and organize themselves into groups of ~20,000 cells. Mathematical models and computational approaches have been a key check on, and guide of, the experimental work. In this minireview, I will discuss diffusion calculations and Monte Carlo simulations that were used for Dictyostelium studies that offer general paradigms for several aspects of cell-cell communication. For instance, computational work showed that diffusible secreted cell-density sensing (quorum) factors can diffuse away so quickly from a single cell that the local concentration will not build up to incorrectly cause the cell to sense that it is in the presence of a high density of other cells secreting that signal. In another example, computation correctly predicted a mechanism that allows a group of cells to break up into subgroups. These are thus some examples of the power and necessity of computational work in biology.

Spot the difference: Causal contrasts in scientific diagrams

An important function of scientific diagrams is to identify causal relationships. This commonly relies on contrasts that highlight the effects of specific difference-makers. However, causal contrast diagrams are not an obvious and easy to recognize category because they appear in many guises. In this paper, four case studies are presented to examine how causal contrast diagrams appear in a wide range of scientific reports, from experimental to observational and even purely theoretical studies. It is shown that causal contrasts can be expressed in starkly different formats, including photographs of complexly visualized macromolecules as well as line graphs, bar graphs, or plots of state spaces. Despite surface differences, however, there is a measure of conceptual unity among such diagrams. In empirical studies they often serve not only to infer and communicate specific causal claims, but also as evidence for them. The key data of some studies is given nowhere except in the diagrams. Many diagrams show multiple causal contrasts in order to demonstrate both that an effect exists and that the effect is specific - that is, to narrowly circumscribe the phenomenon to be explained. In a large range of scientific reports, causal contrast diagrams reflect the core epistemic claims of the researchers.

The protein domains of the Dictyostelium microprocessor that are required for correct subcellular localization and for microRNA maturation

The maturation pathways of microRNAs (miRNAs) have been delineated for plants and several animals, belonging to the evolutionary supergroups of Archaeplastida and Opisthokonta, respectively. Recently, we reported the discovery of the microprocessor complex in Dictyostelium discoideum of the Amoebozoa supergroup. The complex is composed of the Dicer DrnB and the dsRBD (double-stranded RNA binding domain) containing protein RbdB. Both proteins localize at nucleoli, where they physically interact, and both are required for miRNA maturation. Here we show that the miRNA phenotype of a ΔdrnB gene deletion strain can be rescued by ectopic expression of a series of DrnB GFP fusion proteins, which consistently showed punctate perinucleolar localization in fluorescence microscopy. These punctate foci appear surprisingly stable, as they persist both disintegration of nucleoli and degradation of cellular nucleic acids. We observed that DrnB expression levels influence the number of microprocessor foci and alter RbdB accumulation. An investigation of DrnB variants revealed that its newly identified nuclear localization signal is necessary, but not sufficient for the perinucleolar localization. Biogenesis of miRNAs, which are RNA Pol II transcripts, is correlated with that localization. Besides its bidentate RNase III domains, DrnB contains only a dsRBD, which surprisingly is dispensable for miRNA maturation. This dsRBD can, however, functionally replace the homologous domain in RbdB. Based on the unique setup of the Dictyostelium microprocessor with a subcellular localization similar to plants, but a protein domain composition similar to animals, we propose a model for the evolutionary origin of RNase III proteins acting in miRNA maturation.

Towards Gene-Inhibition Therapy: A Review of Progress and Prospects in the Field of Antiviral Antisense Nucleic Acids and Ribozymes

Antisense RNA and its derivatives may provide the basis for highly selective gene inhibition therapies of virus infections. In this review, I concentrate on advances made in the study of antisense RNA and ribozymes during the last five years and their implications for the development of such therapies. It appears that antisense RNAs synthesized at realistic levels within the cell can be much more effective inhibitors than originally supposed. Looking at those experiments that enable comparisons to be made, it seems that inhibitory antisense RNAs are not those that are complementary to particular sites within mRNAs but those that are able to make stable duplexes with their targets, perhaps by virtue of their secondary structure and length. The inclusion of ribozyme sequences within antisense RNAs confers RNA-cleaving activity upon them in vitro and possibly in cells, thereby offering the possibility of markedly increasing their therapeutic potential. The varieties of natural ribozyme and their adaptation as artificial catalysts are reviewed. The implications of these developments for antiviral therapy are discussed.

Cooperative cell motility during tandem locomotion of amoeboid cells

Tandem pairs of Dictyostelium cells migrate synchronously with an ~54-s time delay between the formation of their frontal protrusions. Each cell establishes two active adhesions, with the trailing cell reusing the location of the adhesions of the leading cell. This coordinated motility is mechanically driven and aided by cell–cell adhesions.

Streams of migratory cells are initiated by the formation of tandem pairs of cells connected head to tail to which other cells subsequently adhere. The mechanisms regulating the transition from single to streaming cell migration remain elusive, although several molecules have been suggested to be involved. In this work, we investigate the mechanics of the locomotion of Dictyostelium tandem pairs by analyzing the spatiotemporal evolution of their traction adhesions (TAs). We find that in migrating wild-type tandem pairs, each cell exerts traction forces on stationary sites (∼80% of the time), and the trailing cell reuses the location of the TAs of the leading cell. Both leading and trailing cells form contractile dipoles and synchronize the formation of new frontal TAs with ∼54-s time delay. Cells not expressing the lectin discoidin I or moving on discoidin I–coated substrata form fewer tandems, but the trailing cell still reuses the locations of the TAs of the leading cell, suggesting that discoidin I is not responsible for a possible chemically driven synchronization process. The migration dynamics of the tandems indicate that their TAs’ reuse results from the mechanical synchronization of the leading and trailing cells’ protrusions and retractions (motility cycles) aided by the cell–cell adhesions.

A Simple Retroelement Based Knock-Down System in Dictyostelium: Further Insights into RNA Interference Mechanisms

CHARACTERISTICS OF DIRS-1 MEDIATED KNOCK-DOWNS

We have previously shown that the most abundant Dictyostelium discoideum retroelement DIRS-1 is suppressed by RNAi mechanisms. Here we provide evidence that both inverted terminal repeats have strong promoter activity and that bidirectional expression apparently generates a substrate for Dicer. A cassette containing the inverted terminal repeats and a fragment of a gene of interest was sufficient to activate the RNAi response, resulting in the generation of ~21 nt siRNAs, a reduction of mRNA and protein expression of the respective endogene. Surprisingly, no transitivity was observed on the endogene. This was in contrast to previous observations, where endogenous siRNAs caused spreading on an artificial transgene. Knock-down was successful on seven target genes that we examined. In three cases a phenotypic analysis proved the efficiency of the approach. One of the target genes was apparently essential because no knock-out could be obtained; the RNAi mediated knock-down, however, resulted in a very slow growing culture indicating a still viable reduction of gene expression. ADVANTAGES OF THE DIRS-1–RNAI SYSTEM: The knock-down system required a short DNA fragment (~400 bp) of the target gene as an initial trigger. Further siRNAs were generated by RdRPs since we have shown some siRNAs with a 5'-triphosphate group. Extrachromosomal vectors facilitate the procedure and allowed for molecular and phenotypic analysis within one week. The system provides an efficient and rapid method to reduce protein levels including those of essential genes.

Landscaping plant epigenetics

The understanding of epigenetic mechanisms is necessary for assessing the potential impacts of epigenetics on plant growth, development and reproduction, and ultimately for the response of these factors to evolutionary pressures and crop breeding programs. This volume highlights the latest in laboratory and bioinformatic techniques used for the investigation of epigenetic phenomena in plants. Such techniques now allow genome-wide analyses of epigenetic regulation and help to advance our understanding of how epigenetic regulatory mechanisms affect cellular and genome function. To set the scene, we begin with a short background of how the field of epigenetics has evolved, with a particular focus on plant epigenetics. We consider what has historically been understood by the term "epigenetics" before turning to the advances in biochemistry, molecular biology, and genetics which have led to current-day definitions of the term. Following this, we pay attention to key discoveries in the field of epigenetics that have emerged from the study of unusual and enigmatic phenomena in plants. Many of these phenomena have involved cases of non-Mendelian inheritance and have often been dismissed as mere curiosities prior to the elucidation of their molecular mechanisms. In the penultimate section, consideration is given to how advances in molecular techniques are opening the doors to a more comprehensive understanding of epigenetic phenomena in plants. We conclude by assessing some opportunities, challenges, and techniques for epigenetic research in both model and non-model plants, in particular for advancing understanding of the regulation of genome function by epigenetic mechanisms.

Antisense RNAs and epigenetic regulation

Antisense RNA is the first noncoding RNA found to have a regulatory function. With the advances of biological science, it has been recognized that the function of antisense RNAs is not only limited to post-transcriptional regulation, but extends to transcriptional regulation of various important genes leading to epigenetic changes in DNA methylation and histone modifications. Gene regulation by antisense RNA is a general phenomenon observed in eukaryotic cells while genome-wide natural antisense transcripts have been identified in many animals and plants. Antisense RNAs are not only involved in X-chromosome inactivation and imprinted silencing in normal cells, but aberrantly expressed antisense RNAs can also induce epigenetic silencing of tumor suppressor genes in cancer cells and deletion-induced aberrant antisense RNAs lead to epigenetic silencing and diseases. While a general picture of the pathways involved in antisense RNA-mediated gene regulation has emerged, many questions remain. The mechanisms by which genes are regulated by antisense RNAs, antisense transcript itself is produced and aberrant antisense RNAs induce human diseases are all research focuses of the future.

Inhibition of gene expression in plant cells by expression of antisense RNA

Due to the paucity of mutations in biochemical pathways in plants, an alternative approach to classical genetics was tested by expressing antisense RNA in plant cells. A series of plasmids was constructed with the bacterial gene for chloramphenicol acetyltransferase (EC 2.3.1.28) linked in either the sense or antisense orientation to several different plant gene promoters. Various ratios of sense and antisense chloramphenicol acetyltransferase gene plasmids were introduced into plant protoplasts by electric field-mediated DNA transfer ("electroporation") and the level of expression in each combination was monitored by chloramphenicol acetyltransferase assays. Transcription of antisense RNA was found to effectively block the expression of target genes. Thus, the observation that antisense RNA inhibits gene expression in bacteria and animal systems has been extended to the plant kingdom. Antisense RNA techniques have immediate practical applications in both basic research and in plant genetic engineering.

Stable and heritable inhibition of the expression of nopaline synthase in tobacco expressing antisense RNA

Antisense nopaline synthase (nos) (D-nopaline synthase; EC 1.5.1.19) RNA is stably expressed from the cauliflower mosaic virus 35S promoter in transformed tobacco plants. The expression of a previously introduced wild-type nos gene is inhibited by the antisense RNA, with less nos enzyme activity detected (by a factor of 8-50) depending on the tissue analyzed. The steady-state levels of nos mRNA are reduced in the presence of the antisense RNA, implying that mRNA degradation is probably the main mode of action for the decrease in expression in this system. The antisense RNA-expressing gene and its inhibition of nos expression are shown to be heritable, demonstrating that it is a potentially useful method for the modification of phenotype.

A stable bifunctional antisense transcript inhibiting gene expression in transgenic plants

Tobacco plants expressing constitutive chloramphenicol acetyltransferase (CAT; EC 2.3.1.28) activity were obtained by transformation with a chimeric CAT gene driven by the cauliflower mosaic virus 19S promoter. Plants expressing different levels of CAT activity were retransformed with vectors containing CAT sequences transcriptionally fused in the antisense orientation between the coding region of the hygromycin-resistance gene and the 3' end of the nopaline synthase gene. Several plants regenerated on high concentrations of hygromycin exhibited a loss of CAT activity, whereas plants retransformed with a vector conferring hygromycin resistance but lacking the antisense CAT sequence showed no reduction in CAT activity. RNA blot analysis revealed a strong correlation between the degree of CAT gene inactivation and the levels of stable antisense transcripts accumulated. The possibility that CAT gene inactivation was due to transferred DNA instability was discounted since a kanamycin-resistance gene contiguous with the CAT gene was expressed normally, and DNA blot analysis indicated no loss or rearrangements of the transferred DNA fragments. Thus, the imposed selection pressure enabled the selection of plants expressing high levels of stable bifunctional antisense transcripts that inhibited the activity of the targeted gene.

Discoidin I from Dictyostelium discoideum and Interactions with oligosaccharides: specificity, affinity, crystal structures, and comparison with discoidin II

Discoidin I (DiscI) and discoidin II (DiscII) are N-acetylgalactosamine (GalNAc)-binding proteins from Dictyostelium discoideum. They consist of two domains: an N-terminal discoidin domain and a C-terminal H-type lectin domain. They were cloned and expressed in high yield in recombinant form in Escherichia coli. Although both lectins bind galactose (Gal) and GalNAc, glycan array experiments performed on the recombinant proteins displayed strong differences in their specificity for oligosaccharides. DiscI and DiscII bind preferentially to Gal/GalNAcbeta1-3Gal/GalNAc-containing and Gal/GalNAcbeta1-4GlcNAcbeta1-6Gal/GalNAc-containing glycans, respectively. The affinity of the interaction of DiscI with monosaccharides and disaccharides was evaluated using isothermal titration calorimetry experiments. The three-dimensional structures of native DiscI and its complexes with GalNAc, GalNAcbeta1-3Gal, and Galbeta1-3GalNAc were solved by X-ray crystallography. DiscI forms trimers with involvement of calcium at the monomer interface. The N-terminal discoidin domain presents a structural similarity to F-type lectins such as the eel agglutinin, where an amphiphilic binding pocket suggests possible carbohydrate-binding activity. In the C-terminal H-type lectin domain, the GalNAc residue establishes specific hydrogen bonds that explain the observed affinity (K(d)=3x10(-4) M). The different specificities of DiscI and DiscII for oligosaccharides were rationalized from the different structures obtained by either X-ray crystallography or molecular modeling.

Cell adhesion molecule DdCAD-1 is imported into contractile vacuoles by membrane invagination in a Ca2+- and conformation-dependent manner

The cadA gene in Dictyostelium encodes a Ca(2+)-dependent cell adhesion molecule DdCAD-1 that contains two beta-sandwich domains. DdCAD-1 is synthesized in the cytoplasm as a soluble protein and then transported by contractile vacuoles to the plasma membrane for surface presentation or secretion. DdCAD-1-green fluorescent protein (GFP) fusion protein was expressed in cadA-null cells for further investigation of this unconventional protein transport pathway. Both morphological and biochemical characterizations showed that DdCAD-1-GFP was imported into contractile vacuoles. Time-lapse microscopy of transfectants revealed the transient appearance of DdCAD-1-GFP-filled vesicular structures in the lumen of contractile vacuoles, suggesting that DdCAD-1 could be imported by invagination of contractile vacuole membrane. To assess the structural requirements in this transport process, the N-terminal and C-terminal domains of DdCAD-1 were expressed separately in cells as GFP fusion proteins. Both fusion proteins failed to enter the contractile vacuole, suggesting that the integrity of DdCAD-1 is required for import. Such a requirement was also observed in in vitro reconstitution assays using His(6)-tagged fusion proteins and purified contractile vacuoles. Import of DdCAD-1 was compromised when two of its three Ca(2+)-binding sites were mutated, indicating a role for Ca(2+) in the import process. Spectral analysis showed that mutations in the Ca(2+)-binding sites resulted in subtle conformational changes. Indeed, proteins with altered conformation failed to enter the contractile vacuole, suggesting that the import signal is somehow integrated in the three-dimensional structure of DdCAD-1.

Transformation of Dictyostelium discoideum with plasmid DNA

DNA-mediated transformation is one of the most widely used techniques to study gene function. The eukaryote Dictyostelium discoideum is amenable to numerous genetic manipulations that require insertion of foreign DNA into cells. Here we describe two commonly used methods to transform Dictyostelium cells: calcium phosphate precipitation, resulting in high copy number transformants; and electroporation, an effective technique for producing single integration events into genomic DNA. Single integrations are required for gene disruption by homologous recombination. We also discuss how different selection markers affect vector copy number in transformants and explain why blasticidin has become the preferred selectable marker for making gene knockouts. Both procedures can be accomplished in less than 2 h of hands-on time; however, the calcium phosphate precipitation method contains several incubations, including one of at least 4 h, so the total time required for the transformation is approximately 8 h.

Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum

The traditional view of RNA being merely an intermediate in the transfer of genetic information, as mRNA, spliceosomal RNA, tRNA, and rRNA, has become outdated. The recent discovery of numerous regulatory RNAs with a plethora of functions in biological processes has truly revolutionized our understanding of gene regulation. Tiny RNAs such as microRNAs and small interfering RNAs play vital roles at different levels of gene control. Small nucleolar RNAs are much more abundant than previously recognized, and new functions beyond processing and modification of rRNA have recently emerged. Longer non-coding RNAs (ncRNAs) can also have important regulatory roles in the cell, e.g., antisense RNAs that control their target mRNAs. The majority of these important findings arose from analyses in various model organisms. In this review, we focus on ncRNAs in the social amoeba Dictyostelium discoideum. This important genetically tractable model organism has recently received renewed attention in terms of discovery, regulation and functional studies of ncRNAs. Old and recent findings are discussed and put in context of what we today know about ncRNAs in other organisms.

A cell number-counting factor regulates levels of a novel protein, SslA, as part of a group size regulation mechanism in Dictyostelium

Developing Dictyostelium cells form aggregation streams that break into groups of approximately 2 x 10(4) cells. The breakup and subsequent group size are regulated by a secreted multisubunit counting factor (CF). To elucidate how CF regulates group size, we isolated second-site suppressors of smlA(-), a transformant that forms small groups due to oversecretion of CF. smlA(-) sslA1(CR11) cells form roughly wild-type-size groups due to an insertion in the beginning of the coding region of sslA1, one of two highly similar genes encoding a novel protein. The insertion increases levels of SslA. In wild-type cells, the sslA1(CR11) mutation forms abnormally large groups. Reducing SslA levels by antisense causes the formation of smaller groups. The sslA(CR11) mutation does not affect the extracellular accumulation of CF activity or the CF components countin and CF50, suggesting that SslA does not regulate CF secretion. However, CF represses levels of SslA. Wild-type cells starved in the presence of smlA(-) cells, recombinant countin, or recombinant CF50 form smaller groups, whereas sslA1(CR11) cells appear to be insensitive to the presence of smlA(-) cells, countin, or CF50, suggesting that the sslA1(CR11) insertion affects CF signal transduction. We previously found that CF reduces intracellular glucose levels. sslA(CR11) does not significantly affect glucose levels, while glucose increases SslA levels. Together, the data suggest that SslA is a novel protein involved in part of a signal transduction pathway regulating group size.

Mitochondrial biology and disease in Dictyostelium

The cellular slime mold Dictyostelium discoideum has become an increasingly useful model for the study of mitochondrial biology and disease. Dictyostelium is an amoebazoan, a sister clade to the animal and fungal lineages. The mitochondrial biology of Dictyostelium exhibits some features which are unique, others which are common to all eukaryotes, and still others that are otherwise found only in the plant or the animal lineages. The AT-rich mitochondrial genome of Dictyostelium is larger than its mammalian counterpart and contains 56kb (compared to 17kb in mammals) encoding tRNAs, rRNAs, and 33 polypeptides (compared to 13 in mammals). It produces a single primary transcript that is cotranscriptionally processed into multiple monocistronic, dicistronic, and tricistronic mRNAs, tRNAs, and rRNAs. The mitochondrial fission mechanism employed by Dictyostelium involves both the extramitochondrial dynamin-based system used by plant, animal, and fungal mitochondria and the ancient FtsZ-based intramitochondrial fission process inherited from the bacterial ancestor. The mitochondrial protein-import apparatus is homologous to that of other eukaryote, and mitochondria in Dictyostelium play an important role in the programmed cell death pathways. Mitochondrial disease in Dictyostelium has been created both by targeted gene disruptions and by antisense RNA and RNAi inhibition of expression of essential nucleus-encoded mitochondrial proteins. This has revealed a regular pattern of aberrant mitochondrial disease phenotypes caused not by ATP insufficiency per se, but by chronic activation of the universal eukaryotic energy-sensing protein kinase AMPK. This novel insight into the cytopathological mechanisms of mitochondrial dysfunction suggests new possibilities for therapeutic intervention in mitochondrial and neurodegenerative diseases.

HelF, a putative RNA helicase acts as a nuclear suppressor of RNAi but not antisense mediated gene silencing

We have identified a putative RNA helicase from Dictyostelium that is closely related to drh-1, the 'dicer-related-helicase' from Caenorhabditis elegans and that also has significant similarity to proteins from vertebrates and plants. Green fluorescent protein (GFP)-tagged HelF protein was localized in speckles in the nucleus. Disruption of the helF gene resulted in a mutant morphology in late development. When transformed with RNAi constructs, HelF- cells displayed enhanced RNA interference on four tested genes. One gene that could not be knocked-down in the wild-type background was efficiently silenced in the mutant. Furthermore, the efficiency of silencing in the wild-type was dramatically improved when helF was disrupted in a secondary transformation. Silencing efficiency depended on transcription levels of hairpin RNA and the threshold was dramatically reduced in HelF- cells. However, the amount of siRNA did not depend on hairpin transcription. HelF is thus a natural nuclear suppressor of RNA interference. In contrast, no improvement of gene silencing was observed when mutant cells were challenged with corresponding antisense constructs. This indicates that RNAi and antisense have distinct requirements even though they may share parts of their pathways.

Signal relay during the life cycle of Dictyostelium

A fundamental property of multicellular organisms is signal relay, the process by which information is transmitted from one cell to another. The integration of external information, such as nutritional status or developmental cues, is critical to the function of organisms. In addition, the spatial organizations of multicellular organisms require intricate signal relay mechanisms. Signal relay is remarkably exhibited during the life cycle of the social amoebae Dictyostelium discoideum, a eukaryote that retains a simple way of life, yet it has greatly contributed to our knowledge of the mechanisms cells use to communicate and integrate information. This chapter focuses on the molecules and mechanisms that Dictyostelium employs during its life cycle to relay temporal and spatial cues that are required for survival.

Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi

We have identified a DNA methyltransferase of the Dnmt2 family in Dictyostelium that was denominated DnmA. Expression of the dnmA gene is downregulated during the developmental cycle. Overall DNA methylation in Dictyostelium is ∼0.2% of the cytosine residues, which indicates its restriction to a limited set of genomic loci. Bisulfite sequencing of specific sites revealed that DnmA is responsible for methylation of mostly asymmetric C-residues in the retrotransposons DIRS-1 and Skipper. Disruption of the gene resulted in a loss of methylation and in increased transcription and mobilization of Skipper. Skipper transcription was also upregulated in strains that had genes encoding components of the RNA interference pathway disrupted. In contrast, DIRS-1 expression was not affected by a loss of DnmA but was strongly increased in strains that had the RNA-directed RNA polymerase gene rrpC disrupted. A large number of siRNAs were found that corresponded to the DIRS-1 sequence, suggesting concerted regulation of DIRS-1 expression by RNAi and DNA modification. No siRNAs corresponding to the standard Skipper element were found. The data show that DNA methylation plays a crucial role in epigenetic gene silencing in Dictyostelium but that different, partially overlapping mechanisms control transposon silencing.

Novel non-coding RNAs in Dictyostelium discoideum and their expression during development

The quest for non-coding RNAs (ncRNAs) in the last few years has revealed a surprisingly large number of small RNAs belonging to previously known as well as entirely novel classes. Computational and experimental approaches have uncovered new ncRNAs in all kingdoms of life. In this work, we used a shotgun cloning approach to construct full-length cDNA libraries of small RNAs from the eukaryotic model organism Dictyostelium discoideum. Interestingly, two entirely novel classes of RNAs were identified of which one is developmentally regulated. The RNAs within each class share conserved 5'- and 3'-termini that can potentially form stem structures. RNAs of both classes show predominantly cytoplasmic localization. In addition, based on conserved structure and/or sequence motifs, several of the identified ncRNAs could be divided into classes known from other organisms, e.g. 18 small nucleolar RNA candidates (17 box C/D, of which a few are developmentally regulated, and one box H/ACA). Two ncRNAs showed a high degree of similarity to the small nuclear U2 RNA and signal recognition particle RNA (SRP RNA), respectively. Furthermore, the majority of the regions upstream of the sequences encoding the isolated RNAs share conserved motifs that may constitute new promoter elements.

Chaperonin 60 and mitochondrial disease in Dictyostelium

The single Dictyostelium chaperonin 60 gene, hspA, was cloned, sequenced and characterized. Sequence comparisons and a three-dimensional model for the structure of the encoded protein showed that it exhibits the conserved sequence and structural features expected for its role as the Dictyostelium mitochondrial chaperonin 60. Dictyostelium hspA contains two introns and, unusually for a member of this major heat shock gene family, is not stress-inducible in response to heat, cold or cadmium ions. Although transcription of hspA is down regulated during early Dictyostelium development in response to starvation, the levels of the chaperonin 60 protein remain constant throughout the life cycle. Consistent with the essential role of chaperonin 60 in mitochondrial biogenesis, we were unable to isolate mutants in which the hspA gene had been disrupted. However, transformants were isolated that exhibited differing levels of antisense inhibition of chaperonin 60 expression, depending upon the number of copies of the antisense-expressing plasmid in the genome. Orientation in phototaxis (and thermotaxis) was severely impaired in all antisense transformants, while growth and morphogenesis were markedly defective only in transformants with higher levels of antisense inhibition. This pattern of phenotypes is similar to that reported previously to result from targeted disruption of the mitochondrial large subunit rRNA gene in a subpopulation of mitochondria. This suggests that, regardless of the nature of the underlying genetic defect, mitochondrial deficiency impairs signal transduction more sensitively than other cellular activities.

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.

Gene targets of antisense therapies in breast cancer

Advances in molecular and cell biology have led to further understanding of the mechanisms of malignant growth and metastasis in human breast cancer cells. Initiation and progression of breast cancer results from mutations and the abnormal expression of many genes that control cellular proliferation, differentiation, invasion, metastasis and sensitivity to therapy (chemotherapy and radiation therapy). Inhibition of host immunity also plays a role in breast cancer progression. Many genes have been selected as targets for antisense therapy, including HER-2/neu, PKA, TGF-alpha, EGFR, TGF-beta, IGFIR, P12, MDM2, BRCA, Bcl-2, ER, VEGF, MDR, ferritin, transferrin receptor, IRE, C-fos, HSP27, C-myc, C-raf and metallothionein genes. The strategy behind antisense therapy is the development of specific therapeutic agents that aim to correct the mutations and abnormal expression of cellular genes in breast tumour cells by decreasing gene expression, inducing degradation of target mRNA and causing premature termination of transcription. Many in vitro and in vivo studies have investigated the therapeutic efficacy of oligonucleotides and antisense RNAs. These studies have demonstrated specific inhibition of tumour cell growth by antisense therapy and have shown synergistic inhibitory effects between antisense oligonucleotides or antisense RNA and conventional chemotherapeutic drugs used in the treatment of breast cancer. Antisense oligonucleotides have been modified to improve their ability to penetrate cells, bind to gene sequences and downregulate target gene function. Many delivery systems for antisense RNA and antisense oligonucleotides have been developed, including virus vectors (retrovirus, adenovirus and adeno-associate virus) and liposomes, to carry the antisense RNA or oligonucleotides through the cell membrane into the cytoplasm and nucleus of the tumour cells. However, in order to determine their feasibility antisense therapies need to be further investigated to determine their antitumour activity, pharmacokinetics and toxicity in breast cancer patients.

RNAi in Dictyostelium: the role of RNA-directed RNA polymerases and double-stranded RNase

We show that in Dictyostelium discoideum an endogenous gene as well as a transgene can be silenced by introduction of a gene construct that is transcribed into a hairpin RNA. Gene silencing was accompanied by the appearance of sequence-specific RNA about 23mers and seemed to have a limited capacity. The three Dictyostelium homologues of the RNA-directed RNA polymerase (RrpA, RrpB, and DosA) all contain an N-terminal helicase domain homologous to the one in the dicer nuclease, suggesting exon shuffling between RNA-directed RNA polymerase and the dicer homologue. Only the knock-out of rrpA resulted in a loss of the hairpin RNA effect and simultaneously in a loss of detectable about 23mers. However, about 23mers were still generated by the Dictyostelium dsRNase in vitro with extracts from rrpA(-), rrpB(-), and DosA(-) cells. Both RrpA and a target gene were required for production of detectable amounts of about 23mers, suggesting that target sequences are involved in about 23mer amplification.

Antisense repression in Cryptococcus neoformans as a laboratory tool and potential antifungal strategy

Antisense repression was used as a method to alter gene function in the human-pathogenic fungus Cryptococcus neoformans. The calcineurin A gene (CNA1) and the laccase gene (LAC1) were targeted since disruption of these loci results in phenotypes that are easy to screen (temperature sensitivity and lack of melanin, respectively). Serotype D yeasts were transformed with a plasmid containing the CNA1 cDNA in an antisense orientation under the control of the inducible GAL7 promoter, and serotype A yeasts were transformed with a plasmid containing the LAC1 cDNA in an antisense orientation under the control of the constitutive actin promoter. The calcineurin transformants demonstrated a temperature-sensitive phenotype only when grown on galactose, and the laccase transformants had decreased melanin production. Northern blot analysis of the calcineurin antisense transformants confirmed that the inducible phenotype was associated with a decrease in the native CNA1 transcript levels. Furthermore, it was possible to modestly impair growth of C. neoformans at 37 degrees C by using a 30 bp antisense oligonucleotide targeting CNA1. Antisense repression is now available as a tool for molecular studies in this organism, and may be applicable to other human-pathogenic fungi that have less amenable genetic systems.

Accelerated assessing of antisense RNA efficacy using a chimeric enhanced green fluorescent protein-antisense RNA-producing vector

The selection of suitable parts of a gene as antisense RNA sequences is largely a matter of trial and error and, as a consequence, a rather time-consuming process. In this study, we present a rapid and reproducible method to bypass this protracted procedure by using a chimeric enhanced green fluorescent protein (EGFP)-antisense RNA-producing vector. The combination of a reporter gene and antisense RNA allows easy measurement by flow cytometry of antisense RNA efficacy in successfully transfected cells shortly after transfection. Four chimeric EGFP-p185c-erbB-2-antisense RNA vectors were constructed and transfected into the p185-c-erbB-2-overexpressing cell line SKBR3. Within 1 week, we were able to estimate the inhibitory capacities of the different antisense RNA sequences used in this study. Our results strongly suggest that a chimeric EGFP-antisense RNA vector is an appropriate tool to expedite the laboratory work and time in screening the efficacy of antisense RNA strategies.

Microtubule organization and the effects of GFP-tubulin expression in dictyostelium discoideum

We have labeled microtubules in living Dictyostelium amoebae by incorporation of a GFP-alpha-tubulin fusion protein. The GFP-alpha-tubulin incorporates into microtubules and, as reported by others [Neujahr et al., 1998], the labeled microtubules are highly motile. Electron microscopy (EM) analysis of the distribution and organization of microtubules in the amoebae shows that some cytoplasmic microtubules form close associations. These associations could allow motor proteins attached to one microtubule to walk along an adjacent microtubule and thus generate some of the observed motility. Protein blot analysis indicates that the GFP-alpha-tubulin incorporates into microtubules at a lower efficiency than does the endogenous alpha-tubulin. EM and immunofluorescence (IF) analyses suggest that the GFP-alpha-tubulin interferes with microtubule nucleation. We have also observed an increased sensitivity of the GFP-alpha-tubulin expressing cells to blue light, as compared to wild-type cells. These results suggest that although GFP-alpha-tubulin can be used as a marker for microtubules in living cells, the use of this marker is not recommended for certain types of studies such as assembly dynamics.

gdt1, a new signal transduction component for negative regulation of the growth-differentiation transition in Dictyostelium discoideum

Discoidin I expression was used as a marker to screen for mutants affected in the growth-differentiation transition (GDT) of Dictyostelium. By REMI mutagenesis we have isolated mutant 2-9, an overexpressor of discoidin I. It displays normal morphogenesis but shows premature entry into the developmental cycle. The disrupted gene was denominated gdt1. The mutant phenotype was reconstructed by disruptions in different parts of the gene, suggesting that all had a complete loss of function. gdt1 was expressed in growing cells; the levels of protein and mRNA appear to increase with cell density and rapidly decrease with the onset of development. gdt1 encodes a 175-kDa protein with four putative transmembrane domains. In the C terminus, the derived amino acid sequence displays some similarity to the catalytic domain of protein kinases. Mixing experiments demonstrate that the gdt1(-) phenotype is cell autonomous. Prestarvation factor is secreted at wild-type levels. The response to folate, a negative regulator of discoidin expression, was not impaired in gdt1 mutants. Cells that lack the G protein alpha2 display a loss of discoidin expression and do not aggregate. gdt1(-)/Galpha2(-) double mutants show no aggregation but strong discoidin expression. This suggests that gdt1 is a negative regulator of the GDT downstream of or in a parallel pathway to Galpha2.

Distinct features of post-transcriptional gene silencing by antisense transgenes in single copy and inverted T-DNA repeat loci

The application of antisense transgenes in plants is a powerful tool to inhibit gene expression. The underlying mechanism of this inhibition is still poorly understood. High levels of antisense RNA (as-RNA) are expected to result in strong silencing but often there is no clear correlation between as-RNA levels and the degree of silencing. To obtain insight into these puzzling observations, we have analyzed several petunia transformants of which the pigmentation gene chalcone synthase (Chs) is post-transcriptionally silenced in corollas by antisense (as) Chs transgenes. The transformants were examined with respect to the steady-state as-RNA level, transcription level of the as-transgenes, the repetitiveness and structure of the integrated T-DNAs, and the methylation status of the transgenes. This revealed that the transformants can be divided in two classes: the first class contains a single copy (S) T-DNA of which the as-Chs gene is transcribed, although several-fold lower than the endogenous Chs genes. As there are not sufficient as-RNAs to degrade every mRNA, we speculate that silencing is induced by double-stranded RNA. The second class contains two T-DNAs which are arranged as inverted repeats (IRs). These IR loci are severely methylated and the as-Chs transgenes transcriptionally barely active. The strongest silencing was observed with IR loci in which the as-Chs transgenes were proximal to the centre of the IR. Similar features have been described for co-suppression by IRs composed of sense Chs transgenes, suggesting that silencing by antisense IRs also occurs by co-suppression, either via ectopic DNA pairing or via dsRNA.

Cell cycle-dependent regulation of early developmental genes

Cell cycle phase at the onset of development in Dictyostelium influences cell fate. Cells in the G2 phase, which tend to become spores, show a more rapid induction of expression of the cell surface receptor involved in the chemotaxis. We show that differential induction of developmental expression is restricted to some transcripts, including those encoding proteins required for chemotaxis, and thus is not due to general transcriptional repression during mitosis. We also show that cells showing rapid induction of one such gene are preferentially located at the centre of early aggregates. These results are consistent with cells derived from G2 phase being at the centre of early aggregates because selective differences in gene regulation render them more efficient at aggregation.

Gene identification by shotgun antisense

Shotgun antisense is a technique to make a random set of mutant cells or organisms in such a way that one can select an interesting mutant and then sequence part of the mutated gene within a day. In addition to the fantastic rapidity with which one can identify the mutated gene, there are more advantages of this technique over other mutagenesis techniques: (1) one can identify genes that when completely repressed are lethal; (2) one can select which sets of genes will be mutated; and (3) genes that are expressed from multiple copies can be repressed and thus identified.

Dictyostelium ribosomal protein genes and the elongation factor 1B gene show coordinate developmental regulation which is under post-transcriptional control

Starvation for amino acids initiates the developmental program in the cellular slime mold, Dictyostelium discoideum [19, 20]. One of the earliest developmental events is the decline in ribosomal protein synthesis [2, 17, 29, 30]. The ribosomal protein mRNAs are excluded from polysomes with 20 min to 1 h following the removal of nutrients, and their mRNA levels decline sharply at about 9 h into the 24-h developmental cycle [28, 31, 35, 36]. It has been generally assumed that the decline in r-protein mRNA levels during late development reflected a decline in the transcription rate [12, 32, 43]. Here we demonstrate that this is not the case. The transcription rates of three ribosomal protein genes, rpL11, rpL23 and rpS9 as well as an elongation factor 1B gene have been determined during growth and development in Dictyostelium. Throughout growth and development the transcription rate of the ribosomal protein genes remains relatively constant at 0.2%-0.5% of the rate of rRNA transcription while the elongation factor 1B gene is transcribed at 0.4%-0.6% of the rRNA rate. This low but constant transcription rate is in contrast to a spore coat protein gene Psp D, which is transcribed at 6% of the rRNA rate in late developing cells. The elongation factor 1B gene appears to be co-regulated with the ribosomal protein genes both in terms of its transcription rate and mRNA accumulation. Dictyostelium has been a popular model for understanding signal transduction and the growth to differentiation transition, thus it is of significance that the regulation of ribosome biosynthesis in Dictyostelium resembles that of higher eukaryotes in being regulated largely at the post-transcriptional level in response to starvation as opposed to yeasts where the regulation is largely transcriptional [27].

Protein kinase C beta modulates thrombin-induced Ca2+ signaling and endothelial permeability increase

We investigated the function of the Ca2+-dependent protein kinase C (PKC) beta1 in the regulation of endothelial barrier property. Human dermal microvascular endothelial cells (HMEC-1) were transduced with full-length PKCbeta1 antisense (AS) cDNA or control pLNCX vector to generate stable cell lines (HMEC-AS and HMEC-pLNCX, respectively). Analyses indicated that HMEC-AS expressed the antisense PKCbeta1 transcript with decreased PKCbeta protein level (without a change in PKCalpha or PKCepsilon). The baseline transendothelial 125I-albumin clearance rates of HMEC-1, HMEC-pLNCX, and HMEC-AS were 5.0+/-0.5 x 10(-2), 6.8+/-0.4 x 10(-2), and 6.9+/-0.6 x 10(-2) microl/min, respectively. Activation of HMEC-1 and HMEC-pLNCX with phorbol 12-myristate 13-acetate (PMA) increased the rates to the respective 14.5+/-1.7 x 10(-2) microl/min and 16.9+/-2.8 x 10(-2) microl/min (corresponding to 191% and 149% increases over baseline). However, in HMEC-AS, PMA increased the rate to 9.8+/-1.0 x 10(-2) microl/min (42%). When HMEC-1 and HMEC-pLNCX were activated with thrombin, the rates increased to 10.8+/-1.4 x 10(-2) and 14.0+/-1.9 x 10(-2) microl/min, respectively (116% and 106%). In contrast, thrombin stimulation of HMEC-AS more than doubled the increase to 27.2+/-3.5 x 10(-2) microl/min (294%). Furthermore, the thrombin-induced peak increase in the [Ca2+]i in HMEC-AS was greater than in control cells. Fluorescence-activated cell sorter analysis of thrombin receptor expression indicated that the augmented thrombin-induced responses were not attributable to altered receptor density in HMEC-AS. These results indicate that PKCbeta functions in a negative feedback manner to inactivate thrombin-generated signals and thereby modulates the endothelial permeability increase. Because decreased PKCbeta expression significantly reduced the PMA-induced permeability increase, PKCbeta may downregulate thrombin receptor function upstream of PKC activation (i.e., Ca2+).

Fungal galectins, sequence and specificity of two isolectins from Coprinus cinereus

Galectins are members of a genetically related family of beta-galactoside-binding lectins. At least eight distinct mammalian galectins have been identified. More distantly related, but still conserving amino acid residues critical for carbohydrate-binding, are galectins in chicken, eel, frog, nematode, and sponge. Here we report that galectins are also expressed in a species of fungus, the inky cap mushroom, Coprinus cinereus. Two dimeric galectins are expressed during fruiting body formation which are 83% identical to each other in amino acid sequence and conserve all key residues shared by members of the galectin family. Unlike most galectins, these have no N-terminal post-translational modification and no cysteine residues. We expressed one of these as a recombinant protein and studied its carbohydrate-binding specificity using a novel nonradioactive assay. Binding specificity has been well studied for a number of other galectins, and like many of these, the recombinant C. cinereus galectin shows particular affinity for blood group A structures. These results demonstrate not only that the galectin gene family is evolutionarily much older than previously realized but also that fine specificity for complex saccharide structures has been conserved. Such conservation implies that galectins evolved to perform very basic cellular functions, presumably by interaction with glycoconjugates bearing complex lactoside carbohydrates resembling blood group A.

Antisense and ribozyme constructs in transgenic animals

Geneticists have long sought the ability to add or subtract individual genes from an organism's genome, or to be able to alter the level of expression of a gene in a targeted, developmentally and tissue-specific manner. The development of transgenic technology realized the possibilities of increasing the expression of a specific gene or the transfer of a new gene into an animal. Homologous recombination techniques allow the deletion or alteration of a gene in vivo. The production of transgenic animals incorporating a gene construct that expresses a complimentary antisense RNA to a targeted gene, or an antisense RNA incorporating a catalytic, ribozyme sequence, have been suggested as a potential mechanism for obtaining the developmentally and tissue-specific down-regulation of expression of a targeted gene in vivo. In this paper we review the current literature with respect to the application of antisense and ribozyme constructs in transgenic animals and conclude that such constructs can effectively downregulate the level of mRNA from a target gene, the amount of protein produced in the cell, and result in phenotypic consequences.

Extrachromosomal, homologous expression of trypanothione reductase and its complementary mRNA in Trypanosoma cruzi

Trypanothione reductase (TR), a flavoprotein oxidoreductase present in trypanosomatids but absent in human cells, is regarded as a potential target for the chemotherapy of several tropical parasitic diseases caused by trypanosomes and leishmanias. We investigated the possibility of modulating intracellular TR levels in Trypanosoma cruzi by generating transgenic lines that extrachromosomally overexpress either sense or antisense TR mRNA. Cells overexpressing the sense construct showed a 4-10-fold increase in levels of TR mRNA, protein and enzyme activity. In contrast, recombinant T.cruzi harbouring the antisense construct showed no significant difference in TR protein or catalytic activity when compared with control cells. Although increased levels of TR mRNA were detected in some of the antisense cells neither upregulation nor amplification of the endogenous trypanothione reductase gene (tryA) was observed. Instead, a proportion of plasmid molecules was found rearranged and, as a result, contained the tryA sequence in the sense orientation. Plasmid rescue experiments and sequence analysis of rearranged plasmids revealed that this specific gene inversion event was associated with the deletion of small regions of flanking DNA.

Mutagenesis and gene identification in Dictyostelium by shotgun antisense

We have developed a mutagenesis technique that uses antisense cDNA to identify genes required for development in Dictyostelium discoideum. We transformed Dictyostelium cells with a cDNA library made from the mRNA of vegetative and developing cells. The cDNA was cloned in an antisense orientation immediately downstream of a vegetative promoter, so that in transformed cells the promoter will drive the synthesis of an antisense RNA transcript. We find that individual transformants typically contain one or occasionally two antisense cDNAs. Using this mutagenesis technique, we have generated mutants that fail to aggregate, aggregate but fail to form fruiting bodies, or aggregate but form abnormal fruiting bodies. The individual cDNA molecules from the mutants were identified and cloned using PCR. Initial sequence analysis of the PCR products from 35 mutants has identified six novel Dictyostelium genes, each from a transformant with one antisense cDNA. When the PCR-isolated antisense cDNAs were ligated into the antisense vector and the resulting constructs transformed into cells, the phenotypes of the transformed cells matched those of the original mutants from which each cDNA was obtained. We made homologous recombinant gene disruption transformants for three of the novel genes, in each case generating mutants with phenotypes indistinguishable from those of the original antisense transformants. Shotgun antisense thus is a rapid way to identify genes in Dictyostelium and possibly other organisms.

Antagonistic effects of signal transduction by intracellular and extracellular cAMP on gene regulation in Dictyostelium

In Dictyostelium, cAMP plays a role as an intracellular second messenger and in addition, as an extracellular first messenger. Both functions are thought to be tightly linked because adenylyl cyclase is coupled via G-proteins to the cell surface cAMP receptor cAR 1. Using the discoidin I gene family as a molecular marker for the first stages of development, we show here that induction of transcription requires the G-protein subunit alpha 2 and thus an as yet unidentified surface receptor, CRAC (cytosolic regulator of adenylyl cyclase), and PKA. Induction can be conferred by an increase in intracellular cAMP. In contrast, transcriptional down-regulation occurs by stimulation of cAR 1 with extracellular cAMP and a subsequent, G-protein-independent Ca2+ influx. In a G alpha 2 gene disruption mutant, discoidin I expression can be efficiently modulated by analogues simulating intracellular cAMP (discoidin induction) and extracellular cAMP (discoidin down-regulation). We thus demonstrate possible antagonistic functions of intra- and extracellular cAMP.

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.