A repetitive Dictyostelium gene family that is induced during differentiation and by heat shock

Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1

The retrotransposon DIRS-1 is the most abundant retroelement in Dictyostelium discoideum and constitutes the pericentromeric heterochromatin of the six chromosomes in D. discoideum. The vast majority of cellular siRNAs is derived from DIRS-1, suggesting that the element is controlled by RNAi-related mechanisms. We investigated the role of two of the five Argonaute proteins of D. discoideum, AgnA and AgnB, in DIRS-1 silencing. Deletion of agnA resulted in the accumulation of DIRS-1 transcripts, the expression of DIRS-1-encoded proteins, and the loss of most DIRS-1-derived secondary siRNAs. Simultaneously, extrachromosomal single-stranded DIRS-1 DNA accumulated in the cytoplasm of agnA- strains. These DNA molecules appear to be products of reverse transcription and thus could represent intermediate structures before transposition. We further show that transitivity of endogenous siRNAs is impaired in agnA- strains. The deletion of agnB alone had no strong effect on DIRS-1 transposon regulation. However, in agnA-/agnB- double mutant strains strongly reduced accumulation of extrachromosomal DNA compared with the single agnA- strains was observed.

The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals

Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the function of centromeres, rendering tight retrotransposition control critical to maintaining chromosome integrity. We report that in deletion strains of the RNA-dependent RNA polymerase RrpC, full-length and shorter DIRS-1 messenger RNAs are strongly enriched. Shorter versions of a hitherto unknown long non-coding RNA in DIRS-1 antisense orientation are also enriched in rrpC^– strains. Concurrent with the accumulation of long transcripts, the vast majority of small (21 mer) DIRS-1 RNAs vanish in rrpC^– strains. RNASeq reveals an asymmetric distribution of the DIRS-1 small RNAs, both along DIRS-1 and with respect to sense and antisense orientation. We show that RrpC is required for post-transcriptional DIRS-1 silencing and also for spreading of RNA silencing signals. Finally, DIRS-1 mis-regulation in the absence of RrpC leads to retrotransposon mobilization. In summary, our data reveal RrpC as a key player in the silencing of centromeric retrotransposon DIRS-1. RrpC acts at the post-transcriptional level and is involved in spreading of RNA silencing signals, both in the 5′ and 3′ directions.

Eukaryote DIRS1-like retrotransposons: an overview

Background

DIRS1-like elements compose one superfamily of tyrosine recombinase-encoding retrotransposons. They have been previously reported in only a few diverse eukaryote species, describing a patchy distribution, and little is known about their origin and dynamics. Recently, we have shown that these retrotransposons are common among decapods, which calls into question the distribution of DIRS1-like retrotransposons among eukaryotes.

Results

To determine the distribution of DIRS1-like retrotransposons, we developed a new computational tool, ReDoSt, which allows us to identify well-conserved DIRS1-like elements. By screening 274 completely sequenced genomes, we identified more than 4000 DIRS1-like copies distributed among 30 diverse species which can be clustered into roughly 300 families. While the diversity in most species appears restricted to a low copy number, a few bursts of transposition are strongly suggested in certain species, such as Danio rerio and Saccoglossus kowalevskii.

Conclusion

In this study, we report 14 new species and 8 new higher taxa that were not previously known to harbor DIRS1-like retrotransposons. Now reported in 61 species, these elements appear widely distributed among eukaryotes, even if they remain undetected in streptophytes and mammals. Especially in unikonts, a broad range of taxa from Cnidaria to Sauropsida harbors such elements. Both the distribution and the similarities between the DIRS1-like element phylogeny and conventional phylogenies of the host species suggest that DIRS1-like retrotransposons emerged early during the radiation of eukaryotes.

DIRS1-like retrotransposons are widely distributed among Decapoda and are particularly present in hydrothermal vent organisms

BACKGROUND

Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. Considering their mutational abilities, TEs can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. DIRS1-like retrotransposons are a particular group of retrotransposons according to their mode of transposition that implies a tyrosine recombinase. To date, they have been described in a restricted number of species in comparison with the LTR retrotransposons. In this paper, we determine the distribution of DIRS1-like elements among 25 decapod species, 10 of them living in hydrothermal vents that correspond to particularly unstable environments.

RESULTS

Using PCR approaches, we have identified 15 new DIRS1-like families in 15 diverse decapod species (shrimps, lobsters, crabs and galatheid crabs). Hydrothermal organisms show a particularly great diversity of DIRS1-like elements with 5 families characterized among Alvinocarididae shrimps and 3 in the galatheid crab Munidopsis recta. Phylogenic analyses show that these elements are divergent toward the DIRS1-like families previously described in other crustaceans and arthropods and form a new clade called AlDIRS1. At larger scale, the distribution of DIRS1-like retrotransposons appears more or less patchy depending on the taxa considered. Indeed, a scattered distribution can be observed in the infraorder Brachyura whereas all the species tested in infraorders Caridea and Astacidea harbor some DIRS1-like elements.

CONCLUSION

Our results lead to nearly double both the number of DIRS1-like elements described to date, and the number of species known to harbor these ones. In this study, we provide the first degenerate primers designed to look specifically for DIRS1-like retrotransposons. They allowed for revealing for the first time a widespread distribution of these elements among a large phylum, here the order Decapoda. They also suggest some peculiar features of these retrotransposons in hydrothermal organisms where a great diversity of elements is already observed. Finally, this paper constitutes the first essential step which allows for considering further studies based on the dynamics of the DIRS1-like retrotransposons among several genomes.

The complex repeats of Dictyostelium discoideum

In the course of determining the sequence of the Dictyostelium discoideum genome we have characterized in detail the quantity and nature of interspersed repetitive elements present in this species. Several of the most abundant small complex repeats and transposons (DIRS-1; TRE3-A,B; TRE5-A; skipper; Tdd-4; H3R) have been described previously. In our analysis we have identified additional elements. Thus, we can now present a complete list of complex repetitive elements in D. discoideum. All elements add up to 10% of the genome. Some of the newly described elements belong to established classes (TRE3-C, D; TRE5-B,C; DGLT-A,P; Tdd-5). However, we have also defined two new classes of DNA transposable elements (DDT and thug) that have not been described thus far. Based on the nucleotide amount, we calculated the least copy number in each family. These vary between <10 up to >200 copies. Unique sequences adjacent to the element ends and truncation points in elements gave a measure for the fragmentation of the elements. Furthermore, we describe the diversity of single elements with regard to polymorphisms and conserved structures. All elements show insertion preference into loci in which other elements of the same family reside. The analysis of the complex repeats is a valuable data resource for the ongoing assembly of whole D. discoideum chromosomes.

Changes in cell morphology and actin organization during heat shock in Dictyostelium discoideum: does HSP70 play a role in acquired thermotolerance?

In response to heat shock (34 degrees C, 30 min), cell morphology and actin organization in Dictyostelium discoideum are drastically changed. Loss of pseudopodia and disappearance of F-actin-containing structures were observed by using fluorescence microscopy. These changes were paralleled by a rapid decrease of the F-actin content measured by a TRITC-phalloidin binding assay. The effects of heat shock on cell morphology and actin organization are transient: After heat shock (34 degrees C) or during a long-term heat treatment (30 degrees C), cell morphology, F-actin patterns and F-actin content recovered/adapted to a state which is characteristic for untreated cells. Because F-actin may be stabilized by increased amounts of heat shock proteins, their response and interaction with F-actin was analyzed. After a 1 h heat treatment (34 degrees C), the major heat shock protein of D. discoideum (HSP70) showed maximally increased synthesis rates and levels. During recovery from a 34 degrees C shock or during a continuous heat treatment at 30 degrees C, the HSP70 content first increased and then declined slowly toward normal levels. Pre-treatment of cells with a short heat shock of 30 min at 34 degrees C stabilized the F-actin content when the cells were exposed to a second heat shock. Furthermore, a transient colocalization of HSP70 and actin was observed at the beginning of heat treatment (30 degrees C) using immunological detection of HSP70 in the cytoskeletal actin fraction.

Disruption of glycogen phosphorylase gene expression in Dictyostelium: evidence for altered glycogen metabolism and developmental coregulation of the gene products

Glycogen phosphorylase 1 and 2, the isozymes responsible for glycogen degradation, are encoded by separate genes in Dictyostelium. The two gene products display different transcriptional and translational expression and distinct post-translational regulation. Using DNA-mediated transformation, Dictyostelium clones which lacked either glycogen phosphorylase 1 or 2 (gp1 or gp2) expression were obtained. The loss of either enzyme did not change axenic growth patterns, developmental progression, or gross organismic morphology. In gp1- strains, glycogen accumulated to a 17- to 28-fold higher level during late stationary phase without any obvious detrimental effects. This implies that no alternative pathway for glycogen degradation is present in amoebae, and that glycogen metabolism is not critical for vegetative cell growth. Developmental glycogen concentrations were not altered significantly in any of the transformants, but in gp2- cells the posttranslational regulation of the intact gp1 enzyme was apparently modulated to compensate for the loss of gp2. Western blots of microdissected, lyophilized Dictyostelium slugs and early culminates showed that gp2 was found in both prestalk and prespore cells, with a slight enrichment in prespore cells. The gp1 protein was highly enriched in prestalk cells in the parental strain. In gp2- transformants, however, gp1 was detected in equal amounts in both cell types. The loss of gp2 led to a shift in the cell-type-specific expression pattern of gp1, presumably due to developmental coordinate regulation of gp1 and gp2 at the translational and/or transcriptional level.

Modular transposition and the dynamical structure of eukaryote regulatory evolution

This paper examines a model in which transposable elements provide a modular architecture for the cellular genome, complemented by cellular recombinational transformations, arising in turn as a dynamical consequence of this modular structure. It is proposed that the ecology of transposable elements in a given organism is a function of recombinational protocols of the evolving cellular genome. In mammals this is proposed to involve coordinated meiosis-phased activation of LINEs, SINEs and retrogenes complemented by endogenous retroviral transfer between cells.

The Mu1 transposable element of maize contains two promoter signals recognized by the Escherichia coli RNA polymerase

The galactokinase (GalK) expression plasmid vector system pKO-1 has been used to screen for promoter elements in the maize transposable element Mu1 that function in Escherichia coli. Two transcriptional start points, named S1 and S2, were identified, which are located in the two direct repeats of the transposable element. This paper demonstrates that sequence elements exist in a plant transposable element which function as prokaryotic promotors.

A developmentally regulated membrane protein gene in Dictyostelium discoideum is also induced by heat shock and cold shock

We have analyzed the expression of the Dictyostelium gene P8A7 which had been isolated as a cDNA clone from an early developmentally regulated gene. The single genomic copy generated two mRNAs which were subject to different control mechanisms: while one mRNA (P8A7S) was regulated like the cell-type-nonspecific late genes, the other one (P8A7L) was induced during development, when cells were allowed to attach to a substrate, and when cells were subjected to stress, such as heat shock and cadmium. Interestingly the same induction was also observed with cold shock. RNA processing was inhibited by heat and cold shock, leading to nuclear accumulation of a precursor. The translated region of the cDNA was common to both mRNAs and encoded an unusually hydrophobic peptide with the characteristics of a membrane protein.

Hydrogen peroxide (H2O2) induces actin and some heat-shock proteins in Drosophila cells

Drosophila cells of a clone derived from line Kc were treated with various concentrations of hydrogen peroxide (H2O2). The concentration of 10 mM was lethal, whereas concentrations of 1-100 microM did not affect cell viability, rate of multiplication or protein synthesis. The intermediate concentration of 1 mM H2O2 was used to study the response of the cells to an oxidative stress. We observed a transitory decrease of the global protein synthesis, which was accompanied by changes in the polypeptide pattern. There was a 2.5-fold increase of the synthesis of the heat-shock proteins 70-68 and 23. The most prominent response was a 6.5-fold increase of actin synthesis 3 h after a 1 mM H2O2 treatment. When aminotriazole (an inhibitor of catalase) was added in association with H2O2, the increase of actin synthesis became 8.5-fold. Experiments in which catalase was added at various times after H2O2 showed that a 10-min treatment with H2O2 was sufficient to induce actin and heat-shock protein synthesis 3 h later. H2O2 was shown to induce the transcriptional activation of an actin gene and of the heat-shock protein genes 70 and 23 within minutes. These results are coherent with the hypothesis that the byproducts of O2 reduction (the superoxide ion and hydrogen peroxide) could be inducers of the heat-shock response. Whether the increase of actin synthesis is a stress-related response, and the mode of action of H2O2 are discussed.

A developmentally regulated membrane protein gene in Dictyostelium discoideum is also induced by heat shock and cold shock

We have analyzed the expression of the Dictyostelium gene P8A7 which had been isolated as a cDNA clone from an early developmentally regulated gene. The single genomic copy generated two mRNAs which were subject to different control mechanisms: while one mRNA (P8A7S) was regulated like the cell-type-nonspecific late genes, the other one (P8A7L) was induced during development, when cells were allowed to attach to a substrate, and when cells were subjected to stress, such as heat shock and cadmium. Interestingly the same induction was also observed with cold shock. RNA processing was inhibited by heat and cold shock, leading to nuclear accumulation of a precursor. The translated region of the cDNA was common to both mRNAs and encoded an unusually hydrophobic peptide with the characteristics of a membrane protein.

Heat-shock proteins and development

At the simplest level there is little doubt that the heat shock response is homeostatic, to protect the cell against the ravages of the environmental insult and ensure that the cell can continue its normal life after the crisis has passed.

The 3'-noncoding region of the chick myosin light-chain gene hybridizes to a family of repetitive sequences in the slime mold Dictyostelium discoideum

During studies aimed at isolating myosin-specific genomic clones in Dictyostelium, we probed a lambda genomic library with a chicken myosin light-chain sequence (pML10). Many lambda recombinant Dictyostelium clones hybridized to the pML10 cDNA insert, indicating that this sequence was reiterated in the Dictyostelium genome. It was found that the 3'-noncoding region (pML10-NC) alone was responsible for these results. Dictyostelium DNA contained approximately 65 copies of a sequence(s) similar but not identical to that of pML10-NC. Southern blot analysis showed that pML10-NC hybridized to many Dictyostelium genomic DNA fragments of varying sizes generated by digestion with EcoRI, HindIII, or AluI. In addition, each of the Dictyostelium clones was different in its size, restriction map, and flanking sequences. It seems likely, therefore, that the sequences which hybridized to pML10-NC are scattered throughout the Dictyostelium genome and similar but not identical to each other or to pML10-NC. Thus, probing with pML10-NC has allowed us to select a family of closely related but not identical sequences. These D. discoideum sequences are not found in other slime mold species. No RNA complementary to pML10-NC was found in vegetative cells, 18 h culmination stage, spores, or 1- and 2-h germinating spores. pML10-NC-related sequences were present in two other Dictyostelium species but were absent in the related genus Polysphondylium.

Evidence in a nematode for regulation of transposon excision by tissue-specific factors

The transposable element Tc1 in Caenorhabditis elegans undergoes an excision reaction, which can be detected in a Southern hybridization as the appearance of empty chromosomal insertion sites. This excision reaction is under tissue-specific regulation in that it occurs at much higher frequency in somatic cells than in the germ line. We show here that this regulation is likely to be due to the action of tissue-specific factors that either promote excision in somatic tissues or repress it in the germ line. The rate of excision of elements at five distinct chromosomal sites has been measured by a method that avoids ambiguities due to cell division. All these elements are found to undergo excision at closely similar rates during the L1 larval stage. No distinct difference exists among the elements at different sites that would suggest regulation by flanking sequences.

Characterization of a new repetitive sequence in the Dictyostelium discoideum genome

A repetitive DNA sequence was isolated from a Dictyostelium discoideum genomic plasmid library of BglII-digested DNA ligated to the BamHI site in pBR322. This clone, called pBS582, hybridized to a large number of phage lambda Dictyostelium genomic clones. Southern blot analysis indicated that pBS582 DNA hybridized to many differently sized genomic DNA fragments generated by digestion with Eco RI, AvaI, or HindIII. Restriction maps of pBS582 and five genomic clones showed that the flanking regions of each of the genomic clones were different. These findings indicate that the sequence specific to pBS582 is scattered throughout the Dictyostelium genome and is reiterated approximately 100 times in the haploid genome. Northern blot analysis revealed that RNA which hybridized to pBS582 DNA was present during all stages of growth and development and did not seem to be developmentally regulated. Southern blot analysis of DNAs from other slime molds (D. giganteum, D. purpureum, and Polysphondylium violaceum) were performed to determine whether the pBS582 sequence was present in other species of slime molds. Hybridization of pBS582 was observed to DNA from the two Dictyostelium species but not to Polysphondylium. It may thus be possible to use hybridization of specific sequences as a biochemical tool to study the relatedness of different slime mold species and their molecular taxonomy.

A model for transposon-based eucaryote regulatory evolution

This paper presents a compact model of the role of transposable elements in eucaryote evolution which, although forward looking, is consistent with both experimental results and theories of gene regulation. The model postulates that a principal factor in the emergence of the eucaryotes was the development of a symbiotic relationship between reverse transcribing transposable elements and RNA based gene regulation, which we will call structural symbiosis. Thus, although transposable elements follow their own evolutionary protocol, structural homologies between "cellular" and "viral" genomes result in selective mutagenesis, a situation where transposon mutations are permitted because they can result in phenotypic mutations of the regulatory process with reduced probability of deleterious mutation of structural genes. The incorporation of this scheme into the life cycle of higher organisms results in two forms of integral evolution. Exogenous, in which differing species in an ecosystem share genetic information through viral transfer, and endogenous in which somatically induced regulatory mutations can be mapped back into the germ line.

Dispersed repetitive DNA sequence of Mucor racemosus

A dispersed repetitive DNA sequence has been identified within the genome of the fungus Mucor racemosus. Recombinant phage clones, as well as a plasmid harboring the sequence, have been isolated. Examination of cloned fragments comprising part of the repetitive sequence has led to a partial characterization of the element. The sequence has been detected in other Mucor species, and although the apparent number and chromosomal position of the repetitive sequence vary from strain to strain, it is clear that at least portions of the element have been conserved.

Induction of stress proteins in chicken embryo cells by low-level zinc contamination in amino acid-free media

It has been reported that chicken embryo cells deprived of exogenous amino acids for 4 hours synthesize stress (heat-shock) proteins. Herein, we show that amino acid deprivation is not sufficient to cause induction of stress proteins. Zinc contaminating a component of commercial cell culture medium used to prepare amino acid-free medium was an inducer in our cultures. In the absence of exogenous amino acids, the concentration of zinc ions needed for half-maximal induction of stress proteins was an order of magnitude lower than the dose required for cells in complete medium. Histidine and cystine, which have high affinities for zinc ions, were the amino acids most effective in blocking the induction of stress proteins by zinc. Problems posed by heavy metal ions in culture media and biologic fluids for searches for in vivo inducers of the cellular stress (heat shock) response are discussed.

Transcription of Dictyostelium discoideum transposable element DIRS-1

DIRS-1 is a Dictyostelium discoideum transposable element that contains heat shock promoter sequences in the inverted terminal repeats. We showed that transcription of a 4.5-kilobase polyadenylated RNA initiates at a discrete site within the left-terminal repeat of DIRS-1, downstream from heat shock promoter and TATA box sequences. This RNA represents a full-length transcript of DIRS-1. We describe a cDNA clone that contains the 4.1 kilobases of internal sequence of DIRS-1, a cDNA clone that spans the junction between the internal sequences and the right-terminal repeat, and a cDNA clone that appears to have been transcribed from a rearranged genomic copy of DIRS-1. A second DIRS-1 RNA, named E1, is transcribed on the opposite strand of DIRS-1 from the 4.5-kilobase RNA and is under control of the heat shock promoter in the right-terminal repeat. E1 transcription initiates at multiple positions both within and downstream from the right-terminal repeat. The same transcriptional initiation sites are used during normal development and during heat shock, suggesting that in all cases DIRS-1 transcription is regulated by the heat shock promoters contained within the two terminal repeats.

Dictyostelium transposable element DIRS-1 preferentially inserts into DIRS-1 sequences

Sequence analysis of genomic clones containing the intact Dictyostelium transposable element DIRS-1 reveals that in five of six cases DIRS-1 has inserted into other DIRS-1 sequences. The nucleotide sequences just beyond the endpoints of the terminal repeats of five different genomic clones can be aligned with different regions of the internal nucleotide sequence of DIRS-1. In the three genomic clones which contain flanking sequences on both sides of the element, both flanking sequences are homologous with DIRS-1. In one of these clones, both extended flanking sequences represent the full 4.1-kilobase EcoRI fragment of DIRS-1, which has been interrupted by the insertion of an intact DIRS-1 element. There is no duplication or deletion (except possibly 1 base) of the DIRS-1 sequence upon insertion of a second DIRS-1 transposon. DIRS-1-into-DIRS-1 insertions can occur in either a colinear or inverted orientation with respect to the target sequence; the target sequence need not be an intact DIRS-1 element. We also describe a cDNA clone which could be derived by transcription of a sequence that resulted from a DIRS-1-into-DIRS-1 insertion and discuss its significance concerning the function of the heat-shock promoters found in the terminal repeats of DIRS-1 and in other DIRS-1-related sequences.

The heat shock response

The response of cells to a heat shock or other stresses is the activation of a small number of genes which were previously inactive or transcribed at low levels. This response has been observed in a wide variety of bacterial, plant, and animal species. Evidence is accumulating that at least some of the proteins found in diverse species are similar, indicating a conservation of the response and the proteins in evolution. In a number of organisms a strong positive correlation has been found between the presence of heat shock proteins and ability of the organism to withstand thermal stress. This review attempts to assess the available data concerning the homology of proteins in different species, the localization of the proteins in cells, and the relationship between heat shock proteins and thermoresistance.

Three monoclonal antibodies against measles virus F protein cross-react with cellular stress proteins

In a group of 11 monoclonal antibodies specifically reacting with the measles virus fusion protein, three antibodies also immunoprecipitated other proteins, in particular a 79,000-molecular-weight protein from virus-infected cells. The cross-reacting 79,000-molecular-weight protein was shown to be a virus-induced host stress protein. This protein could be induced by (i) different paramyxoviruses, (ii) heat shock of uninfected HeLa cells, and (iii) 2-deoxyglucose, tunicamycin, or L-canavanine treatment of different mammalian cell lines. Immunofluorescence of stressed HeLa cells localized the cross-reacting host protein(s) mainly in the cytoplasm. The significance of these results in relation to autoimmunity is discussed.

Transcription of Dictyostelium discoideum transposable element DIRS-1

DIRS-1 is a Dictyostelium discoideum transposable element that contains heat shock promoter sequences in the inverted terminal repeats. We showed that transcription of a 4.5-kilobase polyadenylated RNA initiates at a discrete site within the left-terminal repeat of DIRS-1, downstream from heat shock promoter and TATA box sequences. This RNA represents a full-length transcript of DIRS-1. We describe a cDNA clone that contains the 4.1 kilobases of internal sequence of DIRS-1, a cDNA clone that spans the junction between the internal sequences and the right-terminal repeat, and a cDNA clone that appears to have been transcribed from a rearranged genomic copy of DIRS-1. A second DIRS-1 RNA, named E1, is transcribed on the opposite strand of DIRS-1 from the 4.5-kilobase RNA and is under control of the heat shock promoter in the right-terminal repeat. E1 transcription initiates at multiple positions both within and downstream from the right-terminal repeat. The same transcriptional initiation sites are used during normal development and during heat shock, suggesting that in all cases DIRS-1 transcription is regulated by the heat shock promoters contained within the two terminal repeats.

Dictyostelium transposable element DIRS-1 preferentially inserts into DIRS-1 sequences

Sequence analysis of genomic clones containing the intact Dictyostelium transposable element DIRS-1 reveals that in five of six cases DIRS-1 has inserted into other DIRS-1 sequences. The nucleotide sequences just beyond the endpoints of the terminal repeats of five different genomic clones can be aligned with different regions of the internal nucleotide sequence of DIRS-1. In the three genomic clones which contain flanking sequences on both sides of the element, both flanking sequences are homologous with DIRS-1. In one of these clones, both extended flanking sequences represent the full 4.1-kilobase EcoRI fragment of DIRS-1, which has been interrupted by the insertion of an intact DIRS-1 element. There is no duplication or deletion (except possibly 1 base) of the DIRS-1 sequence upon insertion of a second DIRS-1 transposon. DIRS-1-into-DIRS-1 insertions can occur in either a colinear or inverted orientation with respect to the target sequence; the target sequence need not be an intact DIRS-1 element. We also describe a cDNA clone which could be derived by transcription of a sequence that resulted from a DIRS-1-into-DIRS-1 insertion and discuss its significance concerning the function of the heat-shock promoters found in the terminal repeats of DIRS-1 and in other DIRS-1-related sequences.

Repetitive Dictyostelium heat-shock promotor functions in Saccharomyces cerevisiae

The Dictyostelium genome contains 40 copies of a 4.7-kilobase repetitive and apparently transposable DNA sequence (DIRS-1) and about 250 smaller elements that appear to be deletions or rearrangements of DIRS-1. Transcripts of these sequences are induced during differentiation and also by heat shock treatment of growing cells. We showed that one such cloned element, pB41.6 (2.5 kilobases) contains a nucleotide sequence identical to the Drosophila consensus heat shock promotor. To test whether this sequence might indeed control the expression of DIRS-1-related RNAs, we have cloned this genomic segment into yeast cells. In yeast cells, 41.6 directs synthesis of a 1.7-kilobase RNA that is induced at least 10-fold by heat shock. Transcription initiates at about 124 bases 3' of the putative promotor sequence and terminates within the 41.6 insert. A 381-base-pair subclone that contains the putative promotor sequence is sufficient to induce the heat shock response of 41.6 in yeast cells.

Dictyostelium transposable element DIRS-1 has 350-base-pair inverted terminal repeats that contain a heat shock promoter

DIRS-1 is a 4.7-kilobase-pair repetitive and apparently transposable Dictyostelium genetic element that is transcribed during differentiation or after heat shock. The terminal regions of DIRS-1 are inverted repeats of 330 base pairs. The repeats are highly conserved both within a given element as well as between different members of the family (less than 10% divergence). At the distal end of all left repeats is a 32-nucleotide sequence composed almost entirely of A and T residues. In addition to this 32-base A + T sequence, the distal region of all right repeats is extended by a 28-base-pair A + T-rich sequence that is identical in all copies. The sequences flanking each DIRS-1 sequence are completely dissimilar, and there appears to be no duplication of the genomic DNA sequence at the presumed point of DIRS-1 insertion. The terminal repeats can also be found interspersed in the genome independently of the complete element. In addition, the terminal repeats carry a 15-nucleotide sequence that greatly resembles the Drosophila consensus heat shock promoter and may be involved in the transcriptional induction of the DIRS-1 sequences.

Translational control during early Dictyostelium development: possible involvement of poly(A) sequences

A rapid decrease in the translational efficiency of mRNA synthesized during vegetative growth is associated with the initiation of development in Dictyostelium discoideum. In contrast, newly synthesized mRNA associates with polysomes with high efficiency. Discrimination between these two mRNA populations correlates with a rapid shortening of the poly(A) tract on the preexisting mRNA. A model is proposed in which a critical poly(A) length regulates the pattern of protein synthesis by affecting the efficiency with which mRNAs can interact with the translational machinery. The model suggests that transcriptional and translational controls can be coupled by altering the state of adenylation of the preexisting mRNA population. The model allows radical changes in the pattern of protein synthesis without wholesale destruction of preexisting mRNA.

Repetitive Dictyostelium heat-shock promotor functions in Saccharomyces cerevisiae

The Dictyostelium genome contains 40 copies of a 4.7-kilobase repetitive and apparently transposable DNA sequence (DIRS-1) and about 250 smaller elements that appear to be deletions or rearrangements of DIRS-1. Transcripts of these sequences are induced during differentiation and also by heat shock treatment of growing cells. We showed that one such cloned element, pB41.6 (2.5 kilobases) contains a nucleotide sequence identical to the Drosophila consensus heat shock promotor. To test whether this sequence might indeed control the expression of DIRS-1-related RNAs, we have cloned this genomic segment into yeast cells. In yeast cells, 41.6 directs synthesis of a 1.7-kilobase RNA that is induced at least 10-fold by heat shock. Transcription initiates at about 124 bases 3' of the putative promotor sequence and terminates within the 41.6 insert. A 381-base-pair subclone that contains the putative promotor sequence is sufficient to induce the heat shock response of 41.6 in yeast cells.