Differential expression of the members of the discoidin I multigene family during growth and development of Dictyostelium discoideum

Specific cell-cell contact serves as the developmental signal to deactivate discoidin I gene expression in Dictyostelium discoideum

Specific cell-cell contact is a major regulatory signal controlling cell differentiation in Dictyostelium discoideum, causing dramatic changes in the developmental program of gene expression. In this report, we focus on the relationships between specific cell-cell contact and the activity of the genes for discoidin I, an endogenous lectin that has been implicated in the cell-cell cohesion process. By performing quantitative RNA dot-hybridization assays and RNA gel blot-hybridization analyses, using as a probe a recombinant plasmid containing a discoidin I cDNA insert, we have measured changes in discoiding I mRNA levels during normal development and in response to specific manipulations of the state of cellular aggregation. Our major findings are as follows. (i) During normal development on filters, there is a close temporal correspondence between the establishment of specific cell-cell contacts and the decline in discoidin I mRNA levels. By the tight-aggregate stage, discoidin I mRNA is barely detectable. (ii) When tight aggregates are disaggregated and the cells are maintained in the disaggregated state, there is a dramatic rise in discoidin I mRNA content. (iii) When cells are developed in suspension (conditions that interfere with the establishment of tight cell-cell contacts), discoidin I mRNA accumulates to abnormally high levels, and these persist well after the levels in filter-developed cells have declined. Taken together, these results strongly suggest that cell-cell contact is the normal developmental signal to deactivate discoidin I gene expression; thus, a contact-deactivated gene for which a recombinant DNA probe is available has now been identified. Furthermore, we demonstrate that exogenous cAMP almost completely blocks the disaggregation-induced reactivation of discoidin I gene expression. Possible mechanistic relationships between specific cell-cell contact, intracellular cAMP levels, and developmental gene expression are discussed.

Transcriptional pulsing of a developmental gene

It has not been possible to view the transcriptional activity of a single gene within a living eukaryotic cell. It is therefore unclear how long and how frequently a gene is actively transcribed, how this is modulated during differentiation, and how transcriptional events are dynamically coordinated in cell populations. By means of an in vivo RNA detection technique , we have directly visualized transcription of an endogenous developmental gene. We found discrete "pulses" of gene activity that turn on and off at irregular intervals. Surprisingly, the length and height of these pulses were consistent throughout development. However, there was strong developmental variation in the proportion of cells recruited to the expressing pool. Cells were more likely to re-express than to initiate new expression, indicating that we directly observe a transcriptional memory. In addition, we used a clustering algorithm to reveal synchronous transcription initiation in neighboring cells. This study represents the first direct visualization of transcriptional pulsing in eukaryotes. Discontinuity of transcription may allow greater flexibility in the gene-expression decisions of a cell.

Developmental timing in Dictyostelium is regulated by the Set1 histone methyltransferase

Histone-modifying enzymes have enormous potential as regulators of the large-scale changes in gene expression occurring during differentiation. It is unclear how different combinations of histone modification coordinate regimes of transcription during development. We show that different methylation states of lysine 4 of histone H3 (H3K4) mark distinct developmental phases of the simple eukaryote, Dictyostelium. We demonstrate that the enzyme responsible for all mono, di and tri-methylation of H3K4 is the Dictyostelium homolog of the Set1 histone methyltransferase. In the absence of Set1, cells display unusually rapid development, characterized by precocious aggregation of amoebae into multicellular aggregates. Early differentiation markers are abundantly expressed in growing set1 cells, indicating the differentiation program is ectopically activated during growth. This phenotype is caused specifically by the loss of Set1 catalytic activity. Set1 mutants induce premature differentiation in wild-type cells, indicating Set1 regulates production of an extra-cellular factor required for the correct perception of growth conditions. Microarray analysis of the set1 mutants reveals genomic clustering of mis-expressed genes, suggesting a requirement for Set1 in the regulation of chromatin-mediated events at gene clusters.

Dd-STATb, a Dictyostelium STAT protein with a highly aberrant SH2 domain, functions as a regulator of gene expression during growth and early development

Dictyostelium, the only known non-metazoan organism to employ SH2 domain:phosphotyrosine signaling, possesses STATs (signal transducers and activators of transcription) and protein kinases with orthodox SH2 domains. Here, however, we describe a novel Dictyostelium STAT containing a remarkably divergent SH2 domain. Dd-STATb displays a 15 amino acid insertion in its SH2 domain and the conserved and essential arginine residue, which interacts with phosphotyrosine in all other known SH2 domains, is substituted by leucine. Despite these abnormalities, Dd-STATb is biologically functional. It has a subtle role in growth, so that Dd-STATb-null cells are gradually lost from the population when they are co-cultured with parental cells, and microarray analysis identified several genes that are either underexpressed or overexpressed in the Dd-STATb null strain. The best characterised of these,discoidin 1, is a marker of the growth-development transition and it is overexpressed during growth and early development of Dd-STATb null cells. Dimerisation of STAT proteins occurs by mutual SH2 domain:phosphotyrosine interactions and dimerisation triggers STAT nuclear accumulation. Despite its aberrant SH2 domain, the Dd-STATb protein sediments at the size expected for a homodimer and it is constitutively enriched in the nucleus. Moreover, these properties are retained when the predicted site of tyrosine phosphorylation is substituted by phenylalanine. These observations suggest a non-canonical mode of activation of Dd-STATb that does not rely on orthodox SH2 domain:phosphotyrosine interactions.

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.

RasG regulates discoidin gene expression during Dictyostelium growth

Activated rasG, rasG(G12T), was expressed in Dictyostelium cells under the control of the folate-repressible discoidin promoter (pVEII-rasG(G12T)) and found to have a unique pattern of expression when cells were transferred to folate-deficient media: an initial increase of RasG(G12T) resulting from the removal of folate, followed by a rapid decline while cells were still in the early exponential phase of growth. Discoidin levels were considerably lower and declined more rapidly in the pVEII-rasG(G12T) transformant than they did in the wild type, suggesting that RasG(G12T) represses discoidin expression. This was independently confirmed by placing the rasG(G12T) gene under the control of the ribonucleotide reductase (rnrB) promoter. Exposure of cells to 10 mM methyl methanesulfonate (MMS) rapidly generated RasG(G12T) and this was accompanied by an equally rapid decrease in discoidin mRNA levels. rasG null cells also contained decreased levels of discoidin under all conditions tested, indicating that RasG is essential for optimum discoidin expression. However, rasG null cells showed normal regulation of discoidin expression in response to PSF, CMF, folate, bacteria, and axenic media, indicating that RasG is not necessary for any of these responses. These results reveal a role for RasG in regulating discoidin gene expression and add a further level of complexity to the regulation of the discoidin promoter.

The Dictyostelium RasS protein is required for macropinocytosis, phagocytosis and the control of cell movement

Endocytosis and cell migration both require transient localised remodelling of the cell cortex. Several lines of evidence suggest a key regulatory role in these activities for members of the Ras family of small GTPases. We have generated Dictyostelium cells lacking one member of this family, RasS, and the mutant cells are perturbed in endocytosis and cell migration. Mutant amoebae are defective in phagocytosis and fluid-phase endocytosis and are impaired in growth. Conversely, the rasS(-)cells show an enhanced rate of cell migration, moving three times faster than wild-type controls. The mutant cells display an aberrant morphology, are highly polarised, carry many elongated actin protrusions and show a concomitant decrease in formation of pinocytic crowns on the cell surface. These morphological aberrations are paralleled by changes in the actin cytoskeleton, with a significant proportion of the cortical F-actin relocalised to prominent pseudopodia. Rapid migration and endocytosis appear to be mutually incompatible and it is likely that RasS protein is required to maintain the normal balance between these two actin-dependent processes.

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.

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.

Cell-density-dependent repression of discoidin in Dictyostelium discoideum

When Dictyostelium discoideum cells are grown on bacteria, their natural food source, the discoidin genes are induced by cell-density-sensing factors before the food supply is exhausted [11, 18], and expression increases continuously thereafter. This regulation pattern is changed when cells are grown in axenic medium: the discoidins are induced at a considerably lower cell density and are no longer expressed in stationary phase [13]. We have investigated this phenomenon further and show that repression begins when cells are still in exponential growth. It occurs at the level of transcription and involves an element of the discoidin I gamma promoter for which no function has previously been described. Since the effect of high cell density can be mimicked by conditioned medium, it appears that the repression is due to an extracellular signal. This signal is neither ammonia, nor folate, nor cAMP, the known repressors of discoidin expression.

Expression, purification and characterisation of secreted recombinant glycoprotein PsA in Dictyostelium discoideum

Dictyostelium discoideum is a newly developed eukaryotic expression system which is an alternative to tissue cultures for the production of recombinant proteins requiring eukaryotic folding and post-translational modifications. The homologous glycoprotein PsA (prespore specific antigen) is a glycosyl phosphatidylinositol (GPI) anchored membrane protein from D. discoideum. A truncated form of PsA has been expressed in D. discoideum and secreted into a peptone based broth at levels of 10 mg per 1 growth medium. A simple purification protocol for recombinant PsA (rPsA) involved three steps: the concentration of the culture supernatant by ammonium sulfate precipitation, Mono Q anion-exchange chromatography, followed by size exclusion chromatography on Superdex 75. 20 mg of rPsA was purified to 98% purity from 37.1 culture supernatant. Purified rPsA was characterised. The molecular mass of the purified rPsA is 15.6 kDa, which suggests that the molecule is secreted as a monomer and contains 12% (w/w) carbohydrate. The protein sequence of rPsA proved identical to that of the predicted DNA construct. Although the recombinant form of PsA is expressed at a different developmental stage from the native molecule, the same Thr residues that are O-glycosylated in the authentic molecule are glycosylated in the recombinant protein.

Identification and functional analysis of a developmentally regulated extracellular signal-regulated kinase gene in Dictyostelium discoideum

We have cloned a developmentally regulated mitogen-activated protein kinase (extracellular signal-regulated kinase) from Dictyostelium discoideum designated ERK1. Using anti-pTyr antibodies, we show that ERK1 is phosphorylated on tyrosine in vivo and that it will phosphorylate myelin basic protein. The gene expresses two transcripts, one that is preferentially expressed during vegetative growth and early development and one that is induced during the multicellular stages. Developmental Western blots (immunoblots) using anti-ERK1 antibodies indicate that ERK1 is present throughout development. ERK1/lacZ reporter constructs suggest that, in the multicellular stages, the gene is preferentially expressed in a subpopulation of cells scattered throughout the organism, similar to the pattern seen with anterior-like cell markers. Antisense mutagenesis from a derepressible promoter indicates that ERK1 is essential for vegetative growth. Overexpression of ERK1 from either the Actin 15 promoter or the ERK1 promoter results in abnormal morphogenesis starting at the slug stage. Overexpression of ERK1 in null mutants of the phosphotyrosine phosphatase PTP2 results in the production of large aggregation streams and subsequent abnormal morphogenesis that indicate a genetic interaction between ERK1 and PTP2. These cells produce very large aggregation streams that break up into very small mounds that undergo abnormal morphogenesis. The genetic interaction between ERK1 and PTP2 appears to be specific since overexpression of ERK1 in a ptp1- null mutant does not produce the same phenotype. Our results indicate that ERK1 plays an essential role during the growth and differentiation of D. discoideum.

Identification and functional analysis of a developmentally regulated extracellular signal-regulated kinase gene in Dictyostelium discoideum

We have cloned a developmentally regulated mitogen-activated protein kinase (extracellular signal-regulated kinase) from Dictyostelium discoideum designated ERK1. Using anti-pTyr antibodies, we show that ERK1 is phosphorylated on tyrosine in vivo and that it will phosphorylate myelin basic protein. The gene expresses two transcripts, one that is preferentially expressed during vegetative growth and early development and one that is induced during the multicellular stages. Developmental Western blots (immunoblots) using anti-ERK1 antibodies indicate that ERK1 is present throughout development. ERK1/lacZ reporter constructs suggest that, in the multicellular stages, the gene is preferentially expressed in a subpopulation of cells scattered throughout the organism, similar to the pattern seen with anterior-like cell markers. Antisense mutagenesis from a derepressible promoter indicates that ERK1 is essential for vegetative growth. Overexpression of ERK1 from either the Actin 15 promoter or the ERK1 promoter results in abnormal morphogenesis starting at the slug stage. Overexpression of ERK1 in null mutants of the phosphotyrosine phosphatase PTP2 results in the production of large aggregation streams and subsequent abnormal morphogenesis that indicate a genetic interaction between ERK1 and PTP2. These cells produce very large aggregation streams that break up into very small mounds that undergo abnormal morphogenesis. The genetic interaction between ERK1 and PTP2 appears to be specific since overexpression of ERK1 in a ptp1- null mutant does not produce the same phenotype. Our results indicate that ERK1 plays an essential role during the growth and differentiation of D. discoideum.

Altered morphology of vegetative amoebae induced by increased expression of the Dictyostelium discoideum ras-related gene rap1

The rap1 gene of Dictyostelium discoideum is a member of the ras-gene superfamily of low molecular weight GTPase proteins. The rap1 gene is expressed both during growth and development in D. discoideum. To examine the action of the Rap1 protein in D. discoideum, the rap1 cDNA was expressed under the control of the inducible discoidin promoter. Treatment with conditioned media, which induces the discoidin promoter, increased Rap1 protein levels in vegetative cells approximately six fold. Overexpression of the Rap1 protein correlated with the appearance of morphologically aberrant vegetative amoebae: cells were extensively spread and flattened. The distribution of F-actin was altered in these cells, with an increase in actin staining around the cell periphery. Induction of the discoidin promoter by starvation in the rap1 transformants also resulted in spread flat cells. When starved D. discoideum amoebae are refed with HL5 media, the cells rapidly respond by rounding up. By contrast, the rap1 transformant cells showed a pronounced delay in rounding up. Rapid tyrosine phosphorylation of a p45 protein occurred in both control cells and the rap1 transformant upon refeeding, implying that the signal transduction pathway leading to tyrosine phosphorylation remained functional in the rap1 transformant. We propose that the Rap1 protein functions in the regulation of cell morphology in D. discoideum.

Transcriptional regulation by folate: inducible gene expression in Dictyostelium transformants during growth and early development

The Dictyostelium discoidin genes are induced in bacteria-grown cells shortly before the onset of development but are also highly expressed during growth in axenic medium. We here show that axenically growing cells strongly respond to the extracellular signal folate by suppressing discoidin synthesis while cell growth and development is not substantially affected. Repression occurs via two previously identified promoter elements, the dIE and the dAXE. Removal of the signal molecules or setting cells up for development results in rapid reactivation of the promoter. Based on this observation, we constructed the transformation vector pVEII and describe a convenient method which allows for controlled expression of a gene of interest in growing cells and also for external modulation in early development. Deletion constructs of the discoidin promoter can be used in addition to vary transcriptional activity over about one order of magnitude.

The intracisternal A particle derived solo LTR promoter of the rat oncomodulin gene is not present in the mouse gene

The rat gene encoding oncomodulin, a small calcium-binding protein related to parvalbumin, is under the control of a solo long terminal repeat (LTR) derived from an endogenous intracisternal A-particle (IAP). This gene was the first example of a mammalian gene regulated in normal cells by a promoter of retroviral origin (see also article by D. Robins and L. Samuelson in this volume). We show here that the oncomodulin LTR is a member of a small subset of sequence related solo LTR elements present in the rat genome and that a full length IAP genome containing LTRs of this type is no longer present in the rat genome. We have assayed the transcriptional activity of the oncomodulin LTR coupled to the human growth hormone gene as a reporter. Transfections in both Hela cells and 293 cells indicate the oncomodulin LTR promoter is sufficient to efficiently initiate transcription. In 293 cells (human embryo kidney cells transformed with human adenovirus type 5 DNA), the oncomodulin LTR is a strong promoter, capable of bidirectional transcription. Finally, we have determined the structure and the sequence of the mouse oncomodulin gene. Our results suggest that the integration of the IAP particle genome within the rat oncomodulin gene occurred after the rat and the mouse became distinct species.

Developmental regulation of the alpha-mannosidase gene in Dictyostelium discoideum: control is at the level of transcription and is affected by cell density

In Dictyostelium discoideum, there is a group of genes that are expressed following starvation and when exponentially growing cells reach high densities. We have examined the expression of one of these genes, alpha-mannosidase. Using an alpha-mannosidase cDNA probe in Northern (RNA) blot analysis, we have shown that the previously observed increase in alpha-mannosidase enzyme-specific activity during development is due to an increase in the levels of alpha-mannosidase mRNA. mRNA levels reach a maximum by 8 h of development and then begin to decline by 14 to 22 h. Using nuclear run-on analysis, we have found that this gene is regulated at the level of transcription. We also examined the effects of cell-cell contacts, cyclic AMP levels, and protein synthesis on expression of this gene and found that they were not critical in regulating its expression. However, cell density did play a major role in the expression of alpha-mannosidase. High cell density or the presence of buffer conditioned by high-density cells was sufficient to induce expression of alpha-mannosidase, indicating that this is one of the prestarvation response genes. Finally, the alpha-mannosidase gene was not expressed in aggregation-negative mutant strain HMW 404.

Developmental regulation of the alpha-mannosidase gene in Dictyostelium discoideum: control is at the level of transcription and is affected by cell density

In Dictyostelium discoideum, there is a group of genes that are expressed following starvation and when exponentially growing cells reach high densities. We have examined the expression of one of these genes, alpha-mannosidase. Using an alpha-mannosidase cDNA probe in Northern (RNA) blot analysis, we have shown that the previously observed increase in alpha-mannosidase enzyme-specific activity during development is due to an increase in the levels of alpha-mannosidase mRNA. mRNA levels reach a maximum by 8 h of development and then begin to decline by 14 to 22 h. Using nuclear run-on analysis, we have found that this gene is regulated at the level of transcription. We also examined the effects of cell-cell contacts, cyclic AMP levels, and protein synthesis on expression of this gene and found that they were not critical in regulating its expression. However, cell density did play a major role in the expression of alpha-mannosidase. High cell density or the presence of buffer conditioned by high-density cells was sufficient to induce expression of alpha-mannosidase, indicating that this is one of the prestarvation response genes. Finally, the alpha-mannosidase gene was not expressed in aggregation-negative mutant strain HMW 404.

Regulation of the Discoidin I gamma gene in Dictyostelium discoideum: identification of individual promoter elements mediating induction of transcription and repression by cyclic AMP

We dissected the promoter of the developmentally induced and cyclic AMP-repressed discoidin I gamma gene and identified a sequence element essential for developmental induction. Transfer of the element to an inactive heterologous promoter demonstrated that this sequence is sufficient to confer expression in axenically growing cells and to induce gene activity in development after growth on bacteria. A 16-base-pair sequence within this element was shown to be sufficient for induction in the discoidin promoter context and was used to reactivate different truncated promoter constructs. This led to the localization of an element necessary for down regulation of gene expression by extracellular cyclic AMP.

Regulation of the Discoidin I gamma gene in Dictyostelium discoideum: identification of individual promoter elements mediating induction of transcription and repression by cyclic AMP

We dissected the promoter of the developmentally induced and cyclic AMP-repressed discoidin I gamma gene and identified a sequence element essential for developmental induction. Transfer of the element to an inactive heterologous promoter demonstrated that this sequence is sufficient to confer expression in axenically growing cells and to induce gene activity in development after growth on bacteria. A 16-base-pair sequence within this element was shown to be sufficient for induction in the discoidin promoter context and was used to reactivate different truncated promoter constructs. This led to the localization of an element necessary for down regulation of gene expression by extracellular cyclic AMP.

A role for cAMP-dependent protein kinase A in early Dictyostelium development

In Dictyostelium, cAMP functions as an extracellular regulatory molecule that controls aggregation, expression of a number of classes of genes, and cellular differentiation by binding to cell-surface receptors that activate intracellular signal transduction pathways. To investigate possible roles for intracellular cAMP, we have overexpressed the wild-type mouse type-I regulatory subunit (RI) of cAMP-dependent protein C (PKA) in Dictyostelium cells, as well as mutant forms of the subunit that are altered in their ability to bind cAMP. We show that overexpression of a mutated RI, which lacks both cAMP-binding sites and presumably forms a complex with the endogenous Dictyostelium catalytic subunit that cannot be activated by cAMP, results in cells that do not aggregate or express sets of genes that are normally induced in the multicellular stages. Transformations that express the mutant subunit at low levels show no observable phenotype. We show that these cells can respond to pulses of cAMP and activate cAMP receptor/G protein-mediated processes, including the activation of adenylate and guanylate cyclases and the induction of a class of genes known to be regulated through the receptor-mediated pathways; however, the cells do show an altered pattern of expression of other genes normally active during the preaggregation/interphase and aggregation stages. Of interest is a substantial overexpression of the developmentally regulated PDE mRNA. Cell lines carrying constructs encoding the wild-type subunit or mutant subunits lacking one of the two binding sites show no visual phenotype. The results suggest that PKA-mediated functions, presumably controlled by increases in intracellular cAMP, are essential for Dictyostelium aggregation.

Expression and organization of BP74, a cyclic AMP-regulated gene expressed during Dictyostelium discoideum development

We have characterized a cDNA and the corresponding gene for a cyclic AMP-inducible gene expressed during Dictyostelium development. This gene, BP74, was found to be first expressed about the time of aggregate formation, approximately 6 h after starvation. Accumulation of BP74 mRNA did not occur in Dictyostelium cells that had been starved in fast-shaken suspension cultures but was induced in similar cultures to which cyclic AMP pulses had been added. The BP74 cDNA and gene were characterized by DNA sequence analysis and transcriptional mapping. When the BP74 promoter region was fused with a chloramphenicol acetyltransferase reporter gene and reintroduced into Dictyostelium cells, the transfected chloramphenicol acetyltransferase gene displayed the same developmentally regulated pattern of expression as did the endogenous BP74 gene, suggesting that all of the cis-acting elements required for regulated expression were carried by a 2-kilobase cloned genomic fragment. On the basis of sequence analysis, the gene appeared to encode a protein containing a 20-residue hydrophobic sequence at the amino-terminal end and 26 copies of a 20-amino-acid repeat.

Gene amplification associated with the dominant cob-354 cobalt resistance trait in Dictyostelium discoideum

A DNA amplification is correlated with the dominant, unstable cob-354 cobalt resistance trait in the cellular slime mold, Dictyostelium discoideum. The amplified DNA is present as about 50 copies of an extrachromosomal element. Cells grown under nonselective conditions in the absence of cobalt ions lose both the cobalt resistance trait and all extrachromosomal copies of the amplified DNA. The amplified DNA is transferrable to new genetic backgrounds by parasexual genetic crosses. These results explain the inability to map the cob-354 trait to a linkage group. The chromosomal origin of the amplified DNA is group III or VI. Thus the resistance trait appears to be independent of the previously known cobalt resistance locus, cobA, which maps to group VII. A developmental defect involving the production of multiply-tipped aggregates that do not complete fruiting body formation also is correlated with the presence of the amplified DNA.

Expression and organization of BP74, a cyclic AMP-regulated gene expressed during Dictyostelium discoideum development

We have characterized a cDNA and the corresponding gene for a cyclic AMP-inducible gene expressed during Dictyostelium development. This gene, BP74, was found to be first expressed about the time of aggregate formation, approximately 6 h after starvation. Accumulation of BP74 mRNA did not occur in Dictyostelium cells that had been starved in fast-shaken suspension cultures but was induced in similar cultures to which cyclic AMP pulses had been added. The BP74 cDNA and gene were characterized by DNA sequence analysis and transcriptional mapping. When the BP74 promoter region was fused with a chloramphenicol acetyltransferase reporter gene and reintroduced into Dictyostelium cells, the transfected chloramphenicol acetyltransferase gene displayed the same developmentally regulated pattern of expression as did the endogenous BP74 gene, suggesting that all of the cis-acting elements required for regulated expression were carried by a 2-kilobase cloned genomic fragment. On the basis of sequence analysis, the gene appeared to encode a protein containing a 20-residue hydrophobic sequence at the amino-terminal end and 26 copies of a 20-amino-acid repeat.

Retroviral long terminal repeat is the promoter of the gene encoding the tumor-associated calcium-binding protein oncomodulin in the rat

Oncomodulin is a small calcium-binding protein normally found only in extra-embryonic tissues such as the placenta, but whose presence in a variety of tumors has been documented. We have isolated the oncomodulin gene from a Buffalo rat genomic library. The rat gene is approximately 9000 bases in length and consists of five exons and four introns. The introns interrupt the coding sequence of oncomodulin in positions identical with those previously reported for the parvalbumin gene, indicating that the two genes are derived from a common ancestor. Analysis of the promoter sequence of the oncomodulin gene revealed that the gene is under the control of a solo long terminal repeat element related to intracisternal-A particles, a family of endogenous retroviral elements. This represents a unique example of a mammalian gene transcribed in normal and tumor cells, from a promoter of viral origin.

The effects of transcription on the nucleosome structure of four Dictyostelium genes

Micrococcal nuclease digestion of Dictyostelium discoideum nuclei from various developmental stages was used to investigate transcription-related changes in the chromatin structure of the coding region of four genes. Gene activity was determined by Northern blotting and nuclear run on experiments. During strong transcription of the developmentally regulated cysteine proteinase I gene, a smear superimposed on a nucleosomal ladder was observed, indicating perturbation of nucleosomal structure was occurring. However, two other developmentally regulated genes, discoidin I and pSC253, showed only slight nucleosome disruption during high levels of transcription. The chromatin structure of a fourth gene (pCZ22) was disrupted throughout development, even at those stages where transcription was greatly reduced. We suggest that although nucleosome structure can be transiently perturbed by the passage of the transcription complex in vivo, the degree of perturbation and the speed with which nucleosomes reassemble is also influenced by the DNA sequence.

Tissue-specific regulation of human alpha 1-antitrypsin gene expression in transgenic mice

The 5'-flanking sequence of the human alpha 1-antitrypsin (AAT) gene contains multiple cis-regulatory elements, including a distal enhancer and proximal sequences essential for its transcription in cultured hepatoma cells. To understand better the promoter specificity of the AAT gene in vivo, transgenic mice harboring the AAT-SV40 hybrid promoter or the natural AAT promoter fused to a reporter gene (CAT) were generated. Examination of CAT activity in various tissues indicated that the CAT gene was expressed primarily in the liver and also, to a lesser extent, in tissues known to express the AAT gene. In addition, the cis-acting elements of the human AAT gene were utilized to drive the transcription of the SV40 T antigen gene in transgenic mice. Hepatocellular malignancy was found in all founder animals examined, while sporadic occurrence of malignancy was also observed in stomach, pancreas, and kidney. These results verify that the 5'-flanking region of the human AAT gene contains cis-regulatory elements sufficient to confer tissue specificity in vivo.

Molecular analysis of a developmentally regulated gene required for Dictyostelium aggregation

We have previously shown that the developmentally regulated gene D2 is induced during aggregation by pulses of cAMP, which act via the cell surface receptor and consequent signal transduction pathways (W. Rowekamp and R.A. Firtel, 1980, Dev. Biol. 79, 409-418; S.K.O. Mann and R.A. Firtel, 1987, Mol. Cell. Biol. 7, 458-469; S.K.O. Mann, C. Pinko, and R.A. Firtel, 1988, Dev. Biol., in press). In this manuscript, we compare the complete derived amino acid sequence for D2 to two cloned and sequenced eukaryotic esterases and examine the requirement of the D2 gene product for development. Amino acid sequence data comparisons suggest that D2 encodes a serine esterase with strong sequence identity to Torpedo acetylcholine esterase and a Drosophila esterase. The protein has a putative leader sequence, suggesting that it is shunted into vesicles. Using an antisense gene construct driven by a Discoidin I promoter, whose transcriptional activity depends on the growth conditions of the cells, we show that inhibition of D2 mRNA accumulation results in an abnormal developmental program that includes the absence of normal streaming and incomplete aggregate formation and subsequent development. We suggest that D2 encodes an esterase function required for proper aggregation and subsequent development.

Retroviral-mediated gene transfer and expression of human phenylalanine hydroxylase in primary mouse hepatocytes

Genetic therapy for phenylketonuria (severe phenylalanine hydroxylase deficiency) may require introduction of a normal phenylalanine hydroxylase gene into hepatic cells of patients. We report development of a recombinant retrovirus based on the N2 vector for gene transfer and expression of human phenylalanine hydroxylase cDNA in primary mouse hepatocytes. This construct contains an internal promoter of the human alpha 1-antitrypsin gene driving transcription of the phenylalanine hydroxylase cDNA. Primary mouse hepatocytes were isolated from newborn mice, infected with the recombinant virus, and selected for expression of the neomycin-resistance gene. Hepatocytes transformed with the recombinant virus contained high levels of human phenylalanine hydroxylase mRNA transcripts originating form the retroviral and internal promoters. These results demonstrate that the transcriptional regulatory elements of the alpha 1-antitrypsin gene retain their tissue-specific function in the recombinant provirus and establish a method for efficient transfer and high-level expression of human phenylalanine hydroxylase in primary hepatocytes.

The discoidin I gene family of Dictyostelium discoideum is linked to genes regulating its expression

The discoidin I protein has been studied extensively as a marker of early development in the cellular slime mold Dictyostelium discoideum. However, like most other developmentally regulated proteins in this system, no reliable information was available on the linkage of the discoidin genes to other known genes. Analysis of the linkage of the discoidin I genes by use of restriction fragment length polymorphisms revealed that all three discoidin I genes as well as a pseudogene are located on linkage group II. This evidence is consistent with the discoidin I genes forming a gene cluster that may be under the control of a single regulatory element. The discoidin I genes are linked to three genetic loci (disA, motA, daxA) that affect the expression of the discoidin I protein. Linkage of the gene family members to regulatory loci may be important in the coordinate maintenance of the gene family and regulatory loci. A duplication affecting the entire discoidin gene family is also linked to group II; this appears to be a small tandem duplication. This duplication was mapped using a DNA polymorphism generated by insertion of the Tdd-3 mobile genetic element into a Tdd-2 element flanking the gamma gene. A probe for Tdd-2 identified a restriction fragment length polymorphism in strain AX3K that was consistent with generation by a previously proposed Tdd-3 insertion event. A putative duplication or rearrangement of a second Tdd-2 element on linkage group IV of strain AX3K was also identified. This is the first linkage information available for mobile genetic elements in D. discoideum.

Role for DNA replication in beta-globin gene activation

Transcriptional activation of the Xenopus laevis beta-globin gene requires the synergistic action of the simian virus 40 enhancer and DNA replication in DEAE-dextran-mediated HeLa cell transfections. Replication does not act through covalent modification of the template, since its requirement was not obviated by the prior replication of the transfected DNA in eucaryotic cells. Transfection of DNA over a 100-fold range demonstrates that replication does not contribute to gene activation simply increasing template copy number. Furthermore, in cotransfections of replicating and nonreplicating constructs, only replicating templates were transcribed. Replication is not simply a requirement of chromatin assembly, since even unreplicated templates generated nucleosomal ladders. Stimulation of beta-globin transcription by DNA replication, though less marked, was also observed in calcium phosphate transfections. We interpret these results as revealing a dynamic role for replication in gene activation.

Developmental changes in the structural organization of the lectin discoidin I detected by limited proteolysis

Digestion of discoidin I with several proteolytic enzymes reveals the existence of structural domains in this lectin. Significative differences have been detected in the pattern of fragments generated by V8 protease on discoidin I of various developmental situations. The changes observed can be related to the presence of various types of tetrameric structures in discoidin I. Together with the presence of different types of isoforms in vegetative vs. differentiated cells, the results presented here suggest the involvement of different structural organizations in discoidin I which can be related to the biological functions of this lectin.

Establishment of the nuclear location of Dictyostelium discoideum plasmids

The nuclear location of the Dictyostelium discoideum plasmids was studied using a biochemical approach based on the presence of plasmid sequences in nucleosomes. This analysis revealed that all four of the known plasmids (Ddp1, Ddp2, Ddp3, Ddp5) are present in chromatin. This evidence establishes that the D. discoideum plasmids are not cytoplasmic but located in the nucleus. D. discoideum is unique among eukaryotes in possessing a group of nonhomologous endogenous plasmids in its nucleus. These plasmids are excellent starting material for construction of nuclear transformation and expression vectors. Such vectors upon transformation into D. discoideum are also present in chromatin as expected for DNA located in the nucleus.

Two divergently transcribed genes of Dictyostelium discoideum are cyclic AMP-inducible and coregulated during development

The cysteine proteinase 1 (CP1) gene of Dictyostelium discoideum encodes a developmentally regulated sulfhydryl proteinase. We characterized the DNA sequences upstream of the CP1 gene and found a second developmentally regulated gene, which we term DG17. The translational open reading frame of the DG17 gene encoded a 458-amino-acid cysteine- and lysine-rich protein of unknown function. In several regions, the cysteine and lysine residues were arranged in a manner characteristic of the zinc-binding domains found in proteins which interact with nucleic acids. During normal development, the DG17 and CP1 genes are coordinately activated late in aggregation. The addition of exogenous cyclic AMP (cAMP) induced the premature expression of both mRNAs. By measuring the rate of specific mRNA synthesis in isolated nuclei, we showed that cAMP acted at the transcriptional level to activate both genes. The two genes were separated by 910 nucleotides and were divergently transcribed. The intergenic region was predominantly composed of A + T residues except for four short G-rich regions. These sequences coincided with the positions of four nuclease-hypersensitive sites, which appear during aggregation when the DG17 and CP1 genes are transcribed (J. Pavlovic, E. Banz, and R. W. Parish, Nucleic Acids Res. 14:8703-8722, 1986). Two of the G-rich regions formed the core of two almost identical 80-nucleotide repeats located 220 and 320 nucleotides upstream of the CP1 gene. Using the Dictyostelium transformation system, we showed that a restriction fragment containing the intergenic region was capable of directing bidirectional transcription in a cAMP-dependent manner.

Establishment of a transient expression system for Dictyostelium discoideum

We have established a rapid and sensitive transient expression system for Dictyostelium discoideum. We constructed a gene fusion containing the promoter from the Dictyostelium Actin 15 gene fused to the firefly luciferase gene. The enzymatic activity of this gene fusion, expressed at very high levels in stable transformants, was measured to determine optimum conditions for transient expression using electroporation to introduce the DNA into cells. With these conditions, we show that a luciferase gene fusion driven by a prestalk, cell-type specific promoter from the pst-cathepsin gene expresses luciferase at the appropriate developmental stage. In addition, we present results suggesting that the system will be useful for expressing genes in non-axenic cell lines. Finally, we observe that electroporation is more efficient for obtaining stable transformations than the standard calcium phosphate procedure using extrachromosomally replicating shuttle vectors but less efficient for vectors that integrate into the Dictyostelium chromosomes.

Genetics of early Dictyostelium discoideum development

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Role for DNA replication in beta-globin gene activation

Transcriptional activation of the Xenopus laevis beta-globin gene requires the synergistic action of the simian virus 40 enhancer and DNA replication in DEAE-dextran-mediated HeLa cell transfections. Replication does not act through covalent modification of the template, since its requirement was not obviated by the prior replication of the transfected DNA in eucaryotic cells. Transfection of DNA over a 100-fold range demonstrates that replication does not contribute to gene activation simply increasing template copy number. Furthermore, in cotransfections of replicating and nonreplicating constructs, only replicating templates were transcribed. Replication is not simply a requirement of chromatin assembly, since even unreplicated templates generated nucleosomal ladders. Stimulation of beta-globin transcription by DNA replication, though less marked, was also observed in calcium phosphate transfections. We interpret these results as revealing a dynamic role for replication in gene activation.

5' structural motifs and Xenopus beta globin gene activation

We have analysed the structure of the Xenopus beta globin gene 5' flanking region in erythroid and non-erythroid chromatin, in supercoiled plasmids and in minichromosomes assembled in HeLa cell transfections. We have identified two erythroid chromatin-specific, nuclease-hypersensitive sites (HSs), one centred on the cap site, the other located 1000 base-pairs further upstream. An (AT)n tract is located 200 base-pairs upstream from each of these sites. In supercoiled plasmids, the (AT)n tracts, and not the chromatin HSs, are preferentially cleaved by single strand and double strand-specific nucleases. Using restriction enzymes, we have looked at the structure of the cap site HS in minichromosomes assembled in HeLa cell transfections. We find that the structure is indistinguishable from that found in erythroid chromatin, thus reinforcing our previous suggestion, based only on DNase I studies, that the formation of this HS is not dependent on erythroid-specific factors. In view of this close structural mimicry of the situation in vivo, we have used the HeLa cell model system to study the sequences required for cap site HS formation. We find that deletion of the (AT)n tract immediately upstream influenced neither the formation of the HS nor transcription of the globin gene. Indeed, these features remained unaffected by further deletion of upstream sequences, including 50 base-pairs of the HS itself. In this construct, the dimensions of the HS remained the same as in the undeleted construct, with the plasmid sequences that replaced the deleted Xenopus sequences becoming hypersensitive. Thus, HS formation is directed by sequences downstream from --116 acting over a distance of at least 50 base-pairs.

Two divergently transcribed genes of Dictyostelium discoideum are cyclic AMP-inducible and coregulated during development

The cysteine proteinase 1 (CP1) gene of Dictyostelium discoideum encodes a developmentally regulated sulfhydryl proteinase. We characterized the DNA sequences upstream of the CP1 gene and found a second developmentally regulated gene, which we term DG17. The translational open reading frame of the DG17 gene encoded a 458-amino-acid cysteine- and lysine-rich protein of unknown function. In several regions, the cysteine and lysine residues were arranged in a manner characteristic of the zinc-binding domains found in proteins which interact with nucleic acids. During normal development, the DG17 and CP1 genes are coordinately activated late in aggregation. The addition of exogenous cyclic AMP (cAMP) induced the premature expression of both mRNAs. By measuring the rate of specific mRNA synthesis in isolated nuclei, we showed that cAMP acted at the transcriptional level to activate both genes. The two genes were separated by 910 nucleotides and were divergently transcribed. The intergenic region was predominantly composed of A + T residues except for four short G-rich regions. These sequences coincided with the positions of four nuclease-hypersensitive sites, which appear during aggregation when the DG17 and CP1 genes are transcribed (J. Pavlovic, E. Banz, and R. W. Parish, Nucleic Acids Res. 14:8703-8722, 1986). Two of the G-rich regions formed the core of two almost identical 80-nucleotide repeats located 220 and 320 nucleotides upstream of the CP1 gene. Using the Dictyostelium transformation system, we showed that a restriction fragment containing the intergenic region was capable of directing bidirectional transcription in a cAMP-dependent manner.

The expression of two transcripts of the phosphodiesterase gene during the development of Dictyostelium discoideum

One of the earliest events in the development of Dictyostelium discoideum is the induction of the cyclic nucleotide phosphodiesterase gene. During vegetative growth a small amount of secreted phosphodiesterase is synthesized. The phosphodiesterase transcript which is responsible for the vegetative enzyme has a size of 1800 nucleotides. Soon after starvation begins a more abundant mRNA with a size of 2200 nucleotides is synthesized by the developing cells. The induction of the 2200-nucleotide mRNA is dependent on protein synthesis and takes place under all regimens of growth and starvation. When growth is in axenic medium and development is in phosphate buffer, the appearance of the larger transcript is very rapid, occurring within 30 min after the onset of starvation. The initial burst of phosphodiesterase mRNA synthesis is followed by a decline in mRNA abundance unless the cells are stimulated by cAMP. When cells are grown on bacteria and development takes place on filter paper, the larger transcript appears after 4 hr, reaches a peak at 10-12 hr of development, and then slowly disappears. When prestalk and prespore cells from migrating slugs are separated, a small amount of transcript can be found only in the prestalk cells. A series of mutants blocked early in development make very little phosphodiesterase transcript or are otherwise abnormal in expression of the phosphodiesterase mRNA. Together these mutants define five independent genetic loci which affect the accumulation of the phosphodiesterase mRNA. These are the pdsA, fgdA, fgdC, fgdD, and fgdE genes.

Tissue-specific expression of the human alpha 1-antitrypsin gene is controlled by multiple cis-regulatory elements

Human alpha 1-antitrypsin (AAT) is expressed in the liver, and a 318 bp fragment immediately flanking the CAP site of the gene was found to be sufficient to drive the expression of a reporter gene (CAT) specifically in hepatoma cells. The enhancing activity however, was orientation-dependent. The DNA fragment was separated into a distal region and a proximal region. A "core enhancer" sequence GTGGTTTC is present within the distal region and is capable of activity enhancement in both orientations when complemented by the proximal region in the sense orientation. The results strongly suggest that there are multiple cis-acting elements in the human AAT gene that confer cell specificity for its expression. Nuclear proteins prepared from the hepatoma cells bound specifically to the proximal region in a band-shifting assay that was resistant to competition by the globin promoter DNA. Foot-printing analysis showed a protected domain within the proximal region that contains a nearly perfect palindromic sequence TGGTTAATATTCACCA, which may be important in the regulation of AAT expression in the liver.

Structural and functional characterization of a Dictyostelium gene encoding a DIF inducible, prestalk-enriched mRNA sequence

The pDd56 mRNA sequence is highly enriched in prestalk over prespore cells and is inducible by DIF, the putative Dictyostelium stalk-specific morphogen. We show that the pDd56 gene is composed of forty one copies of a twenty four amino acid, cysteine rich repeat. This is highly homologus to a repeat which we have previously shown to compose the major fraction of the pDd63 mRNA, another DIF inducible, prestalk-enriched sequence. The predicted pDd56 protein contains a putative signal peptide but does not appear to contain a transmembrane segment. In combination these features suggest it to be an extrinsic protein and we confirm this elsewhere by showing that the pDd56 gene encodes a known, extracellular protein of the stalk. The pDd56 mRNA is dependent upon exogenous DIF for its accumulation. We show that this control is exerted at the transcriptional level and that a restriction fragment containing 1.7Kb of upstream sequence directs temporally-regulated expression of the gene.

Mouse cell lines that use heat shock promoters to regulate the expression of tissue plasminogen activator

The promoters from Drosophila and human 70,000-dalton heat shock protein (hsp70) genes were linked to human tissue plasminogen activator (tPA) cDNA. Mouse C127 cells were transformed with bovine papilloma virus (BPV) vectors carrying the hybrid hsp70/tPA genes. Stable BPV-transformed cell lines were selected and analyzed for tPA expression before and after heat shock. In most cell lines, there was a low level of tPA production even in the absence of heat shock or other obvious stress. After heat shock (42 degrees C, 2 hr), there was up to a 40-fold increase in tPA production. Production of tPA protein occurred within the first 5 h after the heat shock and was due to a burst of hsp70/tPA transcription during the heat shock. The hsp70/tPA transcripts appeared to have a short half-life. Thus, stable mouse cell lines carrying hsp70/tPA hybrid genes can be induced by a short heat shock to transcribe high levels of hsp70/tPA mRNAs and, subsequently, to produce elevated levels of tPA protein.

Multiple regulatory genes control expression of a gene family during development of Dictyostelium discoideum

Mutant strains of Dictyostelium discoideum carrying dis mutations fail to transcribe specifically the family of developmentally regulated discoidin lectin genes during morphogenesis. The phenotypes of these mutants strongly suggested that the mutations reside in regulatory genes. Using these mutant strains, we showed that multiple regulatory genes are required for the expression of the lectin structural genes and that these regulatory genes (the dis+ alleles) act in trans to regulate this gene family. These regulatory genes fall into two complementation groups (disA and disB) and map to linkage groups II and III, respectively. A further regulatory locus was defined by the identification of an unlinked supressor gene, drsA (discoidin restoring), which is epistatic to disB, but not disA, and results in the restoration of lectin expression in cells carrying the disB mutation. Mutant cells carrying the drsA allele express the discoidin lectin gene family during growth and development, in contrast to wild-type cells which express it only during development. Therefore, the suppressor activity of the drsA allele appears to function by making the expression of the discoidin lectins constitutive and no longer strictly developmentally regulated. The data indicate that normal expression of the discoidin lectins is dependent on the sequential action of the disB+, drsA+, and disA+ gene products. Thus, we described an interacting network of regulatory genes which in turn controls the developmental expression of a family of genes during the morphogenesis of D. discoideum.

Distinct developmental regulation and properties of the responsiveness of different genes to cyclic AMP in Dictyostelium discoideum

Cyclic AMP (cAMP) is known to be an important mediator of gene expression in eukaryotic cells. At present, little is known about the developmental events which render specific genes responsive to cAMP in distinct cell types, or about the biochemical mechanisms by which cAMP exerts these regulatory effects. By examining the effects of cAMP treatment on specific mRNA levels in Dictyostelium discoideum cells with different 'developmental histories', we defined the developmental states in which specific genes display responsiveness to cAMP. We focused on two specific rapid responses: the ability of cAMP to inhibit the expression of an 'early' developmentally regulated mRNA (discoidin-I) and to stimulate the expression of a 'late', prespore-specific mRNA (PL3). Using this approach, we showed that, for both mRNAs, the ability to respond rapidly to cAMP is absent from vegetative cells grown on bacteria, and is acquired during development on filters. Furthermore, we identified several developmental states in which the discoidin-I response to cAMP is present, but in which the PL3 response is not. In experiments designed to examine the effects of cAMP analogues on the levels of these two mRNAs, we demonstrated that the analogue specificities of the discoidin-I and PL3 responses are different, and that the specificity for the PL3 response depends on the developmental state. The developmental kinetics and analogue specificity of the PL3 response suggest a two-step mode of action of cAMP in activating the expression of this gene. We discuss possible implications of these findings for the mechanisms of action of exogenous cAMP as well as for the role of cAMP in controlling the changes in gene expression that accompany normal development.