DNA-mediated transformation in Dictyostelium discoideum: regulated expression of an actin gene fusion

We have constructed a new vector for transformation that carries a fusion of the Dictyostelium discoideum actin 6 promoter gene and 5' flanking region with the bacterial Tn5 NeoR (KanR) gene which can confer resistance to the aminoglycoside G418. This vector can be used to transform D. discoideum cells. Approximately 200 to 2,000 transformants were obtained per 10(7) cells. Transformed cell populations carried vector DNA at an average copy number of ca. 5 per cell, and the DNA was stable for more than 40 generations in the absence of selection. We have shown that transformed cells synthesize functional kanamycin phosphotransferase and that initiation of transcription of the actin 6-NeoR gene fusion occurs at the actin 6 cap site. Moreover, analysis of RNA isolated from transformed and untransformed cells during vegetative growth and during development indicated that the actin 6-NeoR gene fusion was regulated in parallel with the endogenous actin 6 gene, suggesting that the upstream flanking regions of actin 6 contain the cis-acting regulatory sequences sufficient for differential regulation of this gene during D. discoideum development. These results indicate that this system can be used to examine control of gene expression during D. discoideum development.

Site-specific phasing in the chromatin of the rDNA in Dictyostelium discoideum

The rDNA in Dictyostelium discoideum is organized in linear, extrachromosomal, palindromic dimers of approximately 88 X 10(3) bases in length. The dimers are repeated about 90 times per haploid genome. Using indirect end-labeling, we have mapped micrococcal nuclease and DNAase I-sensitive sites in the chromatin near the rDNA telomeres. This region is 3' to the 36 S rRNA coding region and contains a single 5 S rRNA cistron but is primarily non-coding. We have observed somewhat irregularly spaced but specific phasing of nuclease-sensitive sites relative to the underlying DNA sequence. Comparison of the sites in chromatin with those in naked DNA reveals an unusual and striking pattern: the sites in naked DNA that are attacked most readily by both nucleases, presumably because of the specificity of the nucleases for certain sequences or physical characteristics of the DNA, appear to be the same sites that are most protected in chromatin. This pattern extends over most of a 10(4) base region, from the sequence immediately distal to the 36 S rRNA coding region and extending to the terminus. Although much of the sequence-specific phasing is irregularly spaced, salt extraction data are consistent with the presence of nucleosomes. In addition, phasing in the terminal region may be directed partially by proteins that do not bind DNA as tightly as do core histones. We present a model for phasing in spacer regions in which the sequence preferences of nucleases such as micrococcal nuclease and DNAase I may be useful tools in predicting nucleosome placement.

Developmental regulation of a Dictyostelium gene encoding a protein homologous to mammalian ras protein

We have cloned, sequenced, and examined the regulation of a Dictyostelium gene encoding a protein homologous to mammalian ras proteins. The Dictyostelium, yeast, and mammalian proteins have homologous N-terminal regions and less conserved C-terminal regions. We have used DNA probes and a polyclonal antibody to examine the differential accumulation of ras RNA and protein through development. The gene encodes two mRNAs (0.9 and 1.2 kb) that are differentially expressed. The 1.2 kb RNA is found in vegetative cells and disappears rapidly upon initiation of development. Later, both RNAs accumulate preferentially in prestalk cells. The level of the Dd-ras protein remains constant until early culmination and then decreases. Like other prestalk genes, Dd-ras can be induced with cAMP in the absence of cell contact. When aggregated cells are dissociated, both mRNAs decrease. Upon addition of cAMP, the 1.2 kb mRNA reaccumulates at a higher level than that in normal developing cells. The presence of the Dd-ras protein in vegetative cells corroborates other reports suggesting a possible function during cell growth. The sustained level of Dd-ras protein in prestalk cells suggests an additional role during differentiation.

Genomic instability and mobile genetic elements in regions surrounding two discoidin I genes of Dictyostelium discoideum

We have found that the genomic regions surrounding the linked discoidin I genes of various Dictyostelium discoideum strains have undergone rapid changes. Wild-type strain NC-4 has three complete discoidin I genes; its axenic derivative strain Ax-3L has duplicated a region starting approximately 1 kilobase upstream from the two linked genes and extending for at least 8 kilobases past the genes. A separately maintained stock, strain Ax-3K, does not have this duplication but has undergone a different rearrangement approximately 3 kilobases farther upstream. We show that there are repeat elements in these rapidly changing regions. At least two of these elements, Tdd-2 and Tdd-3, have characteristics associated with mobile genetic elements. The Tdd-3 element is found in different locations in related strains and causes a 9- to 10-base-pair duplication of the target site DNA. The Tdd-2 and Tdd-3 elements do not cross-hybridize, but they share a 22-base-pair homology near one end. At two separate sites, the Tdd-3 element has transposed into the Tdd-2 element, directly adjacent to the 22-base-pair homology. The Tdd-3 element may use this 22-base-pair region as a preferential site of insertion.

Conserved structural features are found upstream from the three co-ordinately regulated discoidin I genes of Dictyostelium discoideum

The discoidin I genes of Dictyostelium form a small, co-ordinately regulated multigene family. We have sequenced and compared the upstream regions of the DiscI-alpha, -beta and -gamma genes. For the most part the upstream regions of the three genes are non-homologous. The upstream sequences of the beta and gamma genes are exceedingly A + T-rich, while those of the alpha gene are less so. All three genes have a relatively G + C-rich region 20 to 40 base-pairs in length, found approximately 200 base-pairs 5' to the messenger RNA start site. This G + C-rich region 5' to the beta and gamma genes is flanked by short inverted repeats. Within this region, there is an 11 base-pair exact homology between the alpha and gamma genes, and a less perfect homology between these genes and the beta gene. The homology is flanked at a short distance by interspersed G and T residues. The gamma gene is greater than 90% A + T for greater than 800 base-pairs upstream. Further upstream there is a G + C-rich region that is also found inverted approximately 3.5 X 10(3) base-pairs away. The gamma and beta genes are tandemly linked, and the entire approximately 500 base-pair intergene region between the 3' end of the gamma gene and the 5' end of the beta gene is A + T-rich (approximately 90%) with the exception of the homology region 5' to the gamma gene. We demonstrate also the presence of a discoidin I pseudogene fragment having only 139 base-pairs of discoidin homology with greater than 8% mismatch. It is flanked upstream by five 39 base-pair G + C-rich repeats, and downstream by sequences that are extremely A + T-rich. We discuss the possible significance of the conserved G + C-rich structures on discoidin I gene expression.

An unusual transposon encoding heat shock inducible and developmentally regulated transcripts in Dictyostelium

We have isolated and characterized a transposable element from Dictyostelium discoideum denoted Tdd-1. There are approximately 50 complete copies of the element per haploid genome and approximately 100-150 partial elements. Southern blots of DNA from different Dictyostelium discoideum strains show that Tdd-1 is a mobile element. Tdd-1 is 4.9 kb long, with 313 bp inverted repeats. These repeats lie near the termini, but unlike other transposable elements one end of Tdd-1 extends 36 bp past the repeat and the other extends 1 bp. Tdd-1 encodes a series of developmentally regulated transcripts, all with the same polarity, that increase dramatically in abundance after approximately 10 hr of development. We have also identified a heat shock inducible transcript of the opposite polarity.

Induction and modulation of cell-type-specific gene expression in Dictyostelium

We have identified genes that are expressed preferentially in either prestalk or prespore cells in Dictyostelium. The prestalk mRNAs are detectable at 7.5 hr prior to the completion of cell aggregation, while the prespore mRNAs are not detectable until approximately 15 hr of development. Exogenous cAMP in the absence of sustained cell contact is sufficient to induce prestalk-specific gene expression, while multicellularity is required for the induction of prespore-specific genes. A gene expressed equally in both cell types, which has the same developmental kinetics as the prestalk genes, is induced in shaking culture in the absence of either cAMP or stable cell associations. Dissociation of aggregates results in the rapid loss of prespore- and prestalk-specific mRNAs, and these can be induced to reaccumulate with the addition of cAMP. We conclude that there are substantial differences in the timing and requirements for tissue-specific gene expression in Dictyostelium.

Sequence organization in Dictyostelium: unique structure at the 5'-ends of protein coding genes

We have compared the sequences which lie 5' to the coding regions of 15 Dictyostelium genes transcribed by RNA polymerase II. These sequences are extremely (approximately 90%) A + T rich and contain extensive homopolymeric regions. Like most eukaryotic genes, those in Dictyostelium possess a TATA or Goldberg-Hogness Box approximately 25-35bp 5' to the site of transcription initiation. In addition, each gene contains an oligo (dT) stretch between the TATA Box and mRNA start site; this oligo (dT) sequence is, thus far, unique to Dictyostelium. We suggest that the TATA-oligo (dT) structure is an essential component of the Dictyostelium promoter. The general sequence structure of coding, non-coding and untranscribed flanking regions in Dictyostelium is also discussed.

A DNA-mediated transformation system for Dictyostelium discoideum

We have established a transformation system for Dictyostelium discoideum. The transformation vector contains the protein coding region of the Tn5 neomycin resistance gene fused to the proposed promoter of the Dictyostelium actin 8 gene; the vector also contains a sequence that acts as an autonomously replicating sequence (ars) in yeast. Using this vector, we can transform Dictyostelium vegetative amoebae to be resistant to aminoglycoside G418 at a frequency of between 10(-6) and 10(-4) of the input cells. The transformed cell lines are stable and contain vector sequences integrated within chromosomal DNA.

Differential expression and 5' end mapping of actin genes in Dictyostelium

Using a modification of the Berk and Sharp S1 nuclease mapping procedure and by analyzing actin cDNA clones, we have examined the expression of several members of the 17-member multigene family encoding actin in Dictyostelium. The mapping procedure, which takes advantage of the fact that the actin genes are homologous in the protein-coding region but are very divergent in the proposed 5' untranslated region has enabled us to quantitate the relative expression of several genes during the Dictyostelium life cycle. We have shown that at least six of the 17 potential actin-coding sequences are expressed. One is not expressed at levels of more than 0.5--1% of total actin mRNA at the developmental times examined and appears to be a pseudogene. By quantitating the amount of actin mRNA in mRNA populations isolated from cells at various times in development, we have shown that four of the actin genes show different patterns of expression. Interestingly, three of the four genes appear to encode the same protein. We have also taken advantage of the S1 mapping procedure to identify the 5' ends of the actin mRNAs from four genes and have compared the sequences outside the 5' ends on these genes with the nucleotide sequences of seven other actin genes. We have identified homologous sequences in most of these genes that may be involved in initiation of transcription.

Intervening sequences in a Dictyostelium gene that encodes a low abundance class mRNA

Using S1 nuclease protection experiments and DNA sequencing, we have identified two intervening sequences (introns) within a Dictyostelium gene that codes for a low abundance class mRNA. The two introns are located within the protein coding region of this gene. Both are small (approximately 100 bp) and extremely (approximately 95%) A + T rich. The splice junction sequences are similar to the splice sites in other eukaryotes. Finally, we have shown that these introns are transcribed as part of a higher molecular weight nuclear precursor.

Analysis of the multigene family coding the developmentally regulated carbohydrate-binding protein discoidin-I in D. discoideum

Using recombinant DNA technology, we have isolated chimeric plasmids carrying genomic or cDNA sequences complementary to mRNA encoding the developmentally regulated carbohydrate-binding protein Discoidin-I. The protein is encoded by a 4-5 member multigene family. Mapping of the genomic sequences by DNA blot hybridization suggests that several of the genes are closely linked. RNA excess hybridization kinetics indicate that Discoidin-I mRNA is found in less than one copy per gene per cell during vegetative growth, and increases 500-1000 fold during the first 6 hr of development. The Discoidin-I mRNA concentration decreases during later stages of development. mRNA complementary to the genes shows two bands of -1.0-1.1 kb on acrylamide gels, indicating heterogeneity either in the genes or in mRNA processing.

Unusual nucleotide sequences at the 5' end of actin genes in Dictyostelium discoideum

The nucleotide sequences at the 5' end of one actin cDNA and six actin genomic clones from Dictyostelium have been determined. The amino acid sequences derived from the nucleotide sequences show strong conservation for six of the seven genes relative to the NH2-terminal region of Physarum actin. The region 5' to the AUG initiating codon is greater than 90% A+T residues in all of the genes.

Evidence that populations of Dictyostelium single-copy mRNA transcripts carry common repeat sequences

Two recombinant plasmids, M4 and KH10, carrying Dictyostelium DNA inserted into the Eco RI restriction endonuclease site of pMB9 by poly(dA)-poly(dT) tailing, were selected for study because they are complementary to abundant mRNA populations from Dictyostelium. Both plasmids have been shown to hybridize a heterogeneous size class of mRNAs which, in the case of KH10, comprise 5-10% of the pulse-labeled poly(A)+ RNA from vegetative cells. Analysis of the sequence organization of the two pieces of Dictyostelium DNA shows that they consist mostly of single-copy sequences with a short DNA sequence which is repeated in the genome and interspersed with single-copy DNA. These and other results suggest that the majority of the hybridization of pulse-labeled mRNA to M4 and KH10 is to the short "repeated" DNA sequences. In the genome, members of these repeat families appear to be transcribed onto a population of different single-copy mRNAs. Additional results show that M4 DNA contains a sequence which is entirely complementary to a discrete mRNA.

Dictyostelium rDNA consists of non-chromosomal palindromic dimers containing 5S and 36S coding regions

Restriction enzyme mapping of snap-back DNA has been used to show that the ribosomal DNA (rRNA genes and spacers) from Dictyostelium discoideum exists as 88 kb (kb=1,000 base pairs) linear palindromic dimers. Analysis of the mobility of total cell DNA in 0.15% agarose gels indicates that the majority of the rDNA is not covalently attached to chromosomal DNA.

Identification and analysis of Dictyostelium actin genes, a family of moderately repeated genes

Plasmid M6 has been shown to contain sequences complementary to two related abundant mRNA species which differ in length by 100 nucleotides and code for Dictyostelium actin. M6 complementary RNA was isolated by hybridization to immobilized M6 DNA and translated in vitro. The product is identical to major forms of in vivo labeled actin in both mobility on two-dimensional gels and two-dimensional fingerprints of tryptic peptides. Both plasmid M6 and a second plasmid complementary to the actin mRNA complementary region in M6, pDd actin 2 (McKeown et al., 1978), direct the synthesis in minicells of a number of similar polypeptides that are not seen in minicells containing other recombinant plasmids. Three of these polypeptides are similar in two-dimensional gel mobility to Dictyostelium actin and bind to DNAse I agarose. The repetition frequency of isolated restriction fragments from actin mRNA complementary plasmid M6 has been examined. The data from two different experimental approaches (DNA excess hybridizations using plasmid DNA as probe, and hybridization of plasmid probe to DNA blot filters of restriction enzyme-digested Dictyostelium DNA) indicate that the mRNA complementary region is reiterated 15--20 times. When an actin cDNA probe is used in the same experiments, the results suggest that the entire coding region is reiterated. When the two major actin mRNA species are separated and independently translated, each appears to code for one of the two major actin species. The results suggest that there are at least two different functional genes, and possibly more, for Dictyostelium actin.

Multiple, heterogeneous actin genes in Dictyostelium

We have used an actin gene-containing restriction fragment of plasmid M6 (Kindle and Firtel, 1978) to select a second actin gene-containing plasmid which we have named pDd actin 2. This plasmid has been shown to contain two actin genes separated by 350 bp of nonactin DNA. When heteroduplexes are formed between any two of the three actin genes present in chimeric plasmids, the region of homology is 1100 +/- 100 bp. This is close to the minimum length required to code for actin protein. The 1100 bp region of intergene homology corresponds to the 1100 bp homology observed between M6 and the two actin cDNA plasmids pcDd actin B1 and pcDd actin A1 (Bender et al., 1978). We have no evidence for additional sequences common to either the 3' or 5' ends of the 1100 +/- 100 bp region of intergene homology. Thermal denaturation experiments show that different pairs of actin genes are diverged from each other by as much as 6--8%. There are two size classes of mRNA complementary to the three actin genes. These have lenghts of 1.25 and 1.35 kb as determined on methyl mercuric hydroxide-containing agarose gels. The possible linkage of these three actin genes to other actin genes is discussed.

Regulation of the synthesis of two carbohydrate-binding proteins in Dictyostelium discoideum

The relative rate of de novo synthesis of two membrane-associated carbohydrate-binding proteins (CBP) has been examined during Dictyostelium development. The results show that the relative rate of CBP synthesis is minimal during the vegetative stage and increases to represent approximately 3.5 to 5% of newly synthesized protein during the aggregation stage after which the relative rate decreases. Analysis of the relative rates of synthesis of CBP-26 and CBP-24 indicate that at the peak period of synthesis (approximately 5 to 9 h of development) CBP-26 is synthesized at a rate which is approximately eight times greater than CBP-24. In addition, we have examined the relative amount of CBP-26 and CBP-24 mRNA during development as assayed by its ability to direct CBP synthesis in in vitro protein-synthesizing systems. We show that there is no detectable CBP mRNA in vegetative cells and that during the pre-aggregating stages, assayable CBP mRNA appears and accumulates with a maximal level at the period of peak in vivo CBP synthesis. These results suggest that the rate at CBP synthesis in vivo is controlled by the relative amount of functional mRNA.

Organization of the ribosomal RNA genes of Dictyostelium discoideum: mapping of the nontranscribed spacer regions

Most of the Dictyostelium ribosomal nontranscribed spacer DNA has been mapped using Eco R1, Hind III, and Sal I restriction digests and recombinant plasmids containing parts of the rDNA (ribosomal DNA). The repeat units are at least 42 kb (1 kilobase = 1000 base pairs = 1 kb) long; of this, 8 kb codes for the 36S rRNA precursor. The repeat units give a homogeneous pattern of Sal I, Eco R1, and Hind III restriction fragments. The repeats could be linked by a heterogeneous region in the nontranscribed spacer, not tandemly repeated, or linked in a more complicated structural arrangement. The total rDNA comprises at least 18% of the nuclear DNA.

Structural organization and processing of the genetic transcript in the cellular slime mold Dictyostelium discoideum

The organization of the genome and the synthesis and processing of heterogeneous nuclear RNA (HNRNA) in the cellular slime mold Dictysotelium discoideum have been analyzed. Approximately 60-70% of the genome of Dictyostelium consists of interspersed reiterated and single-copy sequences. The interspersed reiterated sequences have an average length of 250-400 nucleotides. Approximately 50% of the reiterated DNA sequences consist of long noninterspersed sequences. The results of analyses of ynRNA synthesis and processing have been incorporated into a model. According to the model the primary genetic transcript of Dictyostelium is synthesized as a molecule that is 25% larger than mRNA. The bulk of the hnRNA is synthesized from a unit consisting of a short reiterated DNA sequence transcript at the 5' end of the molecule and a single-copy sequence of approximately 1,200 nucleotides in length. In the processing of the mRNA precursor, there appears to be a loss of the majority of the repetitive sequence at the 5' end. The genome contains interspersed sequences of poly (dT)25. These sequences, which appear to be at the 3' terminus of the transcription unit, are transcribed directly into the heterogenous nuclear RNA and are contained within the messenger RNA. During the processing of the heterogeneous nuclear RNA, a poly (A) sequence of approximately 125 nucleotides in length is added posttranscriptionally to the 3' end of the molecule.

Structural organization of the genome of the cellular slime mold Dictyostelium discoideum: interspersion of repetitive and single-copy DNA sequences

The length and interspersion of reiterated and single-copy DNA sequences in Dictyostelium have been examined. The results indicate that approximately 50-60% of the single-copy sequences in DNA fragments 1500 nucleotides long and 75% of the single-copy sequences in fragments 3000 nucleotides long are linked to short interspersed repeat DNA sequences. The average length of these single-copy sequences is 1500 nucleotides. The length of the reiterated DNA has also been analyzed and shows a bimodal distribution. One half is present in sequences greater than 2000 nucleotides long, while the remainder is present as short fragments 250-450 nucleotides long. These shorter fragments are interspersed with the bulk of the single-copy DNA.

Ribonucleoprotein particles containing heterogeneous nuclear RNA in the cellular slime mold Dictyostelium discoideum

As in higher eukaryotes, heterogeneous nuclear RNA (HNRNA) in the cellular slime mold Dictyostelium discoideum is associated with proteins in the form of ribonucleoprotein particles. Mixing experiments with deproteinized hnRNA establish that the nuclear ribonucleoprotein particles are not formed artificially during isolation. In contrast to comparable material from mammalian cells (polydisperse, 40-25- S), Dictyostelium heterogeneous nuclear ribonucleoprotein particles sediment at only 55 S in sucrose gradients, possibly reflecting the smaller size of slime mold hnRNA relative to the large hnRNA found in higher eukaryotes. The RNA of the nuclear 55S ribonucleoprotein particles is shown to be hnRNA by virtue of its size (15S), content of polyadenylate sequences, and hybridization kinetics at DNA excess. The hnRNA-associated porteins are electrophoretically complex and have molecular weights between 20,000 and 150,000. In 0.35 M NaCl most of the proteins are released from the hnRNA. However, a single protein of 72,000-74,000 molecular weight remains bound, as indicated by its co-chromatography with the RNA on poly(U)-Sepharose and banding in Cs2SO4. The same protein is recovered when heterogeneous nuclear ribonucleoprotein is digested with T1 ribonuclease under conditions where the poly(A) is nuclease-resistant. The 73,000 molecular weight protein appears to be specifically bound to polyadenylate sequences in Dictyostelium hrRNA.

Transcription of polydeoxythymidylate sequences in the genome of the cellular slime mold, Dictyostelium discoideum

Messenger RNA of the cellular slime mold, Dictyostelium discoideum, contains about equimolar amounts of two classes of poly(adenylic acid) [poly(A)]; one is about 25 nucleotides long and the second about 100 nucleotides long. At least half of the messenger RNA molecules contain one sequence each of poly(A)(25) and poly(A)(100); both poly(A) sequences are located near the 3' end of messenger RNA, and the kinetics of their appearance on messenger RNA precursor indicates that poly(A)(25) is added before poly(A)(100). Dictyostelium nuclear DNA contains 14,000-15,000 sequences of poly(dT)(25) which could code for the smaller poly(A) residues. The poly(A)(100) must be added post-transcriptionally. The poly(dT)(25) sequences are interspersed throughout the genome and may well represent transcription termination regions.