Spore coat protein synthesis during development of Dictyostelium discoideum requires a low-molecular-weight inducer and continued multicellularity

Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum

BACKGROUND

Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into multicellular organisms. Early phases of the developmental program are often studied in cells starved in suspension while cAMP is provided exogenously. Previous studies revealed massive shifts in the transcriptome under both developmental conditions and a close relationship between gene expression and morphogenesis, but were limited by the sampling frequency and the resolution of the methods.

RESULTS

Here, we combine the superior depth and specificity of RNA-seq-based analysis of mRNA abundance with high frequency sampling during filter development and cAMP pulsing in suspension. We found that the developmental transcriptome exhibits mostly gradual changes interspersed by a few instances of large shifts. For each time point we treated the entire transcriptome as single phenotype, and were able to characterize development as groups of similar time points separated by gaps. The grouped time points represented gradual changes in mRNA abundance, or molecular phenotype, and the gaps represented times during which many genes are differentially expressed rapidly, and thus the phenotype changes dramatically. Comparing developmental experiments revealed that gene expression in filter developed cells lagged behind those treated with exogenous cAMP in suspension. The high sampling frequency revealed many genes whose regulation is reproducibly more complex than indicated by previous studies. Gene Ontology enrichment analysis suggested that the transition to multicellularity coincided with rapid accumulation of transcripts associated with DNA processes and mitosis. Later development included the up-regulation of organic signaling molecules and co-factor biosynthesis. Our analysis also demonstrated a high level of synchrony among the developing structures throughout development.

CONCLUSIONS

Our data describe D. discoideum development as a series of coordinated cellular and multicellular activities. Coordination occurred within fields of aggregating cells and among multicellular bodies, such as mounds or migratory slugs that experience both cell-cell contact and various soluble signaling regimes. These time courses, sampled at the highest temporal resolution to date in this system, provide a comprehensive resource for studies of developmental gene expression.

Control elements of Dictyostelium discoideum prespore specific gene 3B

Expression of the prespore-specific gene 3B in Dictyostelium discoideum Ax-2 cells is first detectable late in development with 3B mRNA levels peaking at 18 h (Corney et al., 1990). Sequence analysis of 3B cDNA and genomic clones revealed two exons, 319bp and 341bp long, separated by an 82bp intron, which encode a 219 residue protein with no significant similarity to any other reported gene product. Transcription starts at an A residue 45bp upstream from the translation initiation codon, preceded by a TATA-like sequence and an oligo-dT stretch. The 5' flanking sequence of the 3B gene is extremely A + T rich but contains five G/C rich stretches, each approximately 7bp long, which have strong sequence similarity to the G boxes found upstream of other developmentally regulated Dictyostelium genes. Analysis of both 3B promoter-CAT reporter gene and 3B promoter-lacZ reporter gene constructs showed that 908bp of 5' flanking sequence is sufficient to confer correct developmental and cell-type specific regulation. Sequential 5' deletion analysis revealed that positive elements lie upstream of position -304 and that negative element(s) lie between positions -264 and -241. Nevertheless, a 286bp promoter fragment containing only sequence located downstream of position -241 directed essentially correct reporter gene expression. Point mutation analysis identified cis-acting elements within this 'sufficient' promoter fragment which activate transcription (G box V and psp-AT type sequences). A short (56bp) region of the 3B promoter sequence containing both G box IV and the psp-AT type element binds two types of nuclear factor, one present in cells throughout development and a second that appears only in late development with a time course comparable to 3B gene induction.

Identification of novel elements which regulate the cell-type specificity of Dictyostelium 7E gene expression

Previously, we have identified the Dictyostelium 7E gene promoter and shown that it is capable of driving expression in the same temporal and cAMP responsive manner as the endogenous gene during development. Furthermore, we have mapped the corresponding transcriptional regulatory sequences within the promoter. In the present study we used the lacZ reporter gene system to examine the role of 7E promoter elements in regulating cell-type specific expression during Dictyostelium morphogenesis. In situ detection of beta-galactosidase activity revealed that expression was induced within anterior prestalk cells at approximately 18 h of development. Subsequently, we found that promoter activity was independently regulated in subpopulations of prestalk cells. Element(s) upstream of position - 532 were necessary for expression in pstA cells while more proximal elements (located downstream of position - 426) were capable of directing expression in pstO cells. Deletion of a G-rich element ('GGT' box; 5'-GGT GAT GA-3') located between positions - 159 and - 152 resulted both in a loss of expression in pstA cells and aberrant expression in the prespore zone. Furthermore, the spatial organisation of reporter gene expression directed by this construct during culmination delineated a population of cells that have not been previously defined. These data suggest that the 7E gene is independently regulated in subpopulations of prestalk cells during development.

The carboxyl terminus of Dictyostelium discoideum protein 1I encodes a functional glycosyl-phosphatidylinositol signal sequence

The 1I gene is expressed in the prespore cells of culminating Dictyostelium discoideum. The open reading frame of 1I cDNA encodes a protein of 155 amino acids with hydrophobic segments at both its NH(2)- and COOH-termini that are indicative of a glycosyl-phosphatidylinositol (GPI)-anchored protein. A hexaHis-tagged form of 1I expressed in D. discoideum cells appeared on Western blot analysis as a doublet of 27 and 24 kDa, with a minor polypeptide of 22 kDa. None of the polypeptides were released from the cell surface with bacterial phosphatidylinositol-specific phospholipase C, although all three were released upon nitrous acid treatment, indicating the presence of a phospholipase-resistant GPI anchor. Further evidence for the C-terminal sequence of 1I acting as a GPI attachment signal was obtained by replacing the GPI anchor signal sequence of porcine membrane dipeptidase with that from 1I. Two constructs of dipeptidase with the 1I GPI signal sequence were constructed, one of which included an additional six amino acids in the hydrophilic spacer. Both of the resultant constructs were targeted to the surface of COS cells and were GPI-anchored as shown by digestion with phospholipase C, indicating that the Dictyostelium GPI signal sequence is functional in mammalian cells. Site-specific antibodies recognising epitopes either side of the expected GPI anchor attachment site were used to determine the site of GPI anchor attachment in the constructs. These parallel approaches show that the C-terminal signal sequence of 1I can direct the addition of a GPI anchor.

A developmentally regulated gene encodes the dictyostelium homolog of yeast ribosomal protein S4 and mammalian LLRep3 proteins

We report the sequence and expression of a single-copy gene from Dictyostelium discoideum which encodes the homolog of yeast ribosomal protein S4, a protein located on the small ribosomal subunit and known to play an important role in maintaining translational fidelity. Over a highly conserved central region, the Dictyostelium protein has 78% sequence similarity to the yeast protein and 83% sequence similarity to mammalian S4 protein homologs, the LLRep3 proteins. The Dictyostelium gene encodes a polypeptide 28,717 Da in size and hence this ribosomal protein has been named rp29. The N-terminal sequence of the Dictyostelium rp29 protein is extended by 61 amino acids and 14 amino acids compared to the mammalian and yeast proteins, respectively, and the C-terminus is correspondingly 15 amino acids or 2 amino acids shorter. Although the coding region of the rp29 gene is present on a single exon, a 157bp intron interrupts the 5' untranslated region and unusually contains four direct repeats of the sequence TCAATCT. The gene is expressed maximally during vegetative growth but a second peak of expression also occurs late in development which is restricted to prestalk cells; rp29 is the first Dictyostelium ribosomal protein gene reported which shows prestalk-specific developmental expression. During each round of expression, only a single 0.9kb transcript is produced which is similar in size to the yeast S4 ribosomal protein transcript (0.8kb) but markedly smaller than the mammalian LLRep3 mRNA (1.7kb) due to a much shorter 5' untranslated region.

DC6, a novel type of Dictyostelium discoideum gene regulated by secreted factors but not by cAMP

We have isolated a gene, DC6, which is induced in the early aggregative stages of development in Dictyostelium discoideum. The increase in DC6 expression is dependent on high cell density, indicating that cellular interactions are required for DC6 induction. In low-cell-density cultures, the induction of DC6 occurs if supplied with conditioned medium of developing cells, suggesting that secreted factors are involved in DC6 induction. The expression of DC6 is not affected (1) in the presence of caffeine or adenosine, which block the production or the action of cAMP pulses, (2) in the presence of high concentrations of cAMP, or (3) in mutant strains (Synag7 and FrigidA), which are defective in transduction pathways of cAMP pulse signals. These results indicate that the induction of DC6 does not require extracellular cAMP pulse signals, which are known to regulate the expression of many genes in the early development. Independence of cAMP signals and dependence on other unknown cellular interactions are prominent characteristics of DC6.

Evidence for the presence of a growth factor in Dictyostelium discoideum

Polypeptide hormones, recognized for their ability to regulate cell growth and differentiation, have been classified as growth factors. These growth factors have been extensively described in higher eukaryotic organisms and cell lines [Hedin and Westermark, Cell 37:9-20, 1984]. Here we report the identification and partial characterization of a putative growth factor present in vegetative amoebae of the cellular slime mold Dictyostelium discoideum. A mutant was selected and found to be temperature sensitive due to the absence of an extracellular protein suggestive of a growth factor. The putative growth factor (DGF) is a protein resistant to both heat and strong detergent treatment but sensitive to reducing agents. The physiological significance of DGF is as yet unknown. DGF is of interest both in relation to understanding the events which control cell proliferation in Dictyostelium and in its relationship to other known growth factors.

Cell-type-specific genes expressed late in Dictyostelium development show markedly different responses to 3'5' cyclic AMP

The maintenance of late gene expression by 3'5' cyclic AMP was re-examined using several newly isolated cell-type-specific genes. Expression of all the prespore-enriched genes ceased immediately upon disaggregation of developing cells and pre-existing mRNA was rapidly degraded. For most genes, cAMP had little or no effect either alone or in combination with conditioned medium factors. The expression of the non-cell-type-specific genes 7E and 2C also ceased upon cell disaggregation but cAMP triggered a full re-induction of expression although the timing of the response differed markedly between these two genes. In contrast to earlier interpretations, these data argue that for none of these late prespore genes is cAMP alone sufficient for the maintenance of expression. The responses of the two prestalk mRNAs examined were gene-specific. Prestalk 5D mRNA decayed slowly upon disaggregation and was partially stabilized by cAMP whereas prestalk 5G mRNA increased upon disaggregation and was inhibited by cAMP.

Developmental expression and characterization of the gene encoding spore coat protein SP60 in Dictyostelium discoideum

The complete coding sequence, upstream sequence and developmental expression of Dictyostelium discoideum AX2 spore coat protein gene SP60 is reported. The gene contains two exons, 154bp and 1121bp long, separated by a 119bp intron, and encodes a protein of 46,925 molecular weight plus a 23-amino-acid hydrophobic leader sequence. The N-terminus of the mature protein consists of four copies of a perfect hexapeptide repeat (GDWNNN). The central region is rich in cysteine residues, including four highly conserved cysteine-rich repeats with homology to 'EGF-like' repeats. The C-terminus is aspartate-rich and composed of multiple imperfect copies of a D(G/D)DYD repeat followed by several repeats of the tetrapeptide DNDW and derived sequences. A TATA box promoter motif juxtaposed to an oligo(dA) stretch lies 52bp upstream of the main transcriptional start site of the gene. Six AC-rich boxes occur in the region -327 to -556, all of which contain the consensus sequence CACAC. Two GC-rich boxes and a C-rich element (TTACCCCA) are also present upstream. Another open reading frame is positioned a short distance downstream of the SP60 gene in the opposite transcriptional orientation. Expression of the SP60 gene ceases upon disaggregation to single cells and cannot be restored by high levels of extracellular cAMP either alone or in combination with conditioned medium factors.

Developmental regulation of cell-type-enriched mRNAs in Dictyostelium discoideum

We describe sixteen new families of cDNA clones representing mRNAs that are expressed preferentially in either prespore or prestalk cells during development of Dictyostelium discoideum and two new mRNAs that are expressed in a non-cell-type-specific manner. None of the prespore-enriched mRNAs are detectable in Dictyostelium cells until 13-15 h of development but then they increase dramatically and peak at 18-22 h. Upon dissociation of developing aggregates, all these mRNAs rapidly decay to low levels. In marked contrast to data presented for prespore genes by other workers, cyclic AMP either has no effect on the mRNA levels in dissociated cells or is only weakly effective in restoring normal expression. A prestalk-enriched mRNA examined, 5G mRNA, is similarly expressed late in development but is also expressed in vegetative cells. The level of 5G mRNA is only moderately affected by cell disaggregation.

Relationships between cell-cell interactions, cAMP, and gene expression in a developmental mutant of Dictyostelium discoideum

Previous work has led us to propose that close cell-cell associations during D. discoideum development serve as a signal to deactivate expression of discoidin I mRNA, and that intracellular cAMP serves as a mediator of this regulatory pathway. This model is based in part on the failure of a morphogenetic mutant, EB-21, to deactivate discoidin I expression under conditions where these cells fail to acquire cell-cell cohesiveness and hence remain as single cells, unlike the wild type strain which forms multicellular aggregates. Here we show that the failure of EB-21 to express specific cohesiveness depends on developmental conditions, and that under conditions where close cell-cell associations are allowed to form, discoidin I mRNA expression is deactivated normally. Furthermore, in both wild type and EB-21 there is a close correlation between formation close cell-cell associations and elevation of intracellular cAMP under different developmental conditions. Additional analyses of the biological behavior of EB-21 indicate that it acquires a normal cAMP chemotactic signal-response system, and that the morphogenetic defect cannot be corrected by co-development with wild type cells. The results are discussed in terms of possible relationships between cell-cell interactions, cAMP metabolism, and developmental gene expression in this organism.

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.

Identification and analysis of the regulation of a prestalk cell-surface antigen of Dictyostelium discoideum

The properties of two differentiation antigens, rsa 4.2 and rsa 3.1, were examined. Both appear on the cell surface early in differentiation, but they differ with respect to their cell-type specificity. rsa 4.2 appears 1-2 h after differentiation has begun and is present on all cells during all stages of differentiation. In contrast, rsa 3.1 appears after 1-2 h on all aggregating amebae and later becomes restricted to prestalk cells. The pattern of regulation of rsa 3.1 indicates that this prestalk antigen appears on all cells early in differentiation but disappears in cells that differentiate along the prespore pathway. As a result, only cells in the anterior of migrating slugs carry this antigen. Predictions of two competing models of Dictyostelium pattern formation, i.e., position-dependent differentiation and random, position-independent differentiation, were tested by flow cytometry and immunochemical staining of sections of cells at the mound and mound-with-tip stages. Our results do not rule out either model, although they are incompatible with the simplest interpretation of the model for position-independent differentiation. The results clearly indicate that cells that ultimately differentiate along the spore pathway pass through an earlier cell state that includes the presence of a prestalk cell-surface antigen identified as rsa 3.1.

Changes during differentiation in requirements for cAMP for expression of cell-type-specific mRNAs in the cellular slime mold, Dictyostelium discoideum

A number of genes encoding developmentally regulated mRNAs in the cellular slime mold, Dictyostelium discoideum, have been described. Many of these are regulated by cAMP. Analysis of the earliest time at which elevated levels of cAMP can induce the expression of these mRNAs reveals a more complex pattern of regulation in which genes change in their ability to be induced in response to cAMP with developmental stage. A prestalk mRNA (C1/D11) previously thought not be regulated by elevated levels of cAMP is inducible by cAMP between aggregation and loose mound stage; later in development its expression becomes independent of elevated cAMP. The early prespore genes (prespore class I) also show two modes of regulation; early in development they are induced independently of continuous elevated levels of cAMP, while later in development their expression is dependent upon elevated cAMP. The period during development when the prestalk genes are cAMP inducible precedes by 2 hr the first time at which either the early prespore class I or late prespore class II mRNAs are inducible by continuous elevated levels of cAMP. Previous analysis of these mRNAs has been carried out using Dictyostelium cells grown axenically. In this report we have studied the developmental expression of these mRNAs in cells grown on bacteria. A substantial shutoff of the class I prestalk and early prespore (class I) mRNAs not seen in axenically grown cells is observed when bacterially grown cells are plated for development. Less than 10% of the maximal level of these mRNAs remains in the cells at the time of mature spore and stalk differentiation. Additionally, in the bacterially grown cells two distinct patterns of developmental regulation are observed for mRNAs which in axenically growing cells appear to be constitutively expressed throughout growth and development.

Cyclic AMP and NH3/NH4+ both regulate cell-type-specific mRNA accumulation in the cellular slime mold, Dictyostelium discoideum

Dictyostelium discoideum cells plated for development until aggregation stage, and then dissociated into media containing glucose, albumin, and cAMP will form into clumps and undergo prespore and prestalk differentiation. Differentiation in this in vitro system is dependent on three components: cAMP, multicellularity, and the acquisition of "differentiation competence" which the cells acquire in a period between interphase and aggregation stage when plated on Millipore filters. We have used this system to explore aspects of the multicellular environment which are involved in regulation the accumulation of the different prespore- and prestalk-specific messenger RNAs. Two classes of prespore messenger RNA, as well as a prestalk-specific messenger RNA, all require the acquisition of differentiation competence in order to be expressed in response to cAMP. Additionally, all of these messenger RNAs require agglomerate formation for maximal expression. The addition of 33 mM ammonium sulfate (NH4)2SO4, however, can entirely replace the requirement for agglomerate formation for expression of the prestalk-specific messenger RNA, and can partially substitute for agglomerate formation in inducing the expression of both classes of prespore-specific messenger RNAs. In this system, cAMP is essential for the initial induction of expression of all three classes of messenger RNAs. In this system, cAMP is essential for the initial induction of expression of all three classes of messenger RNAs while agglomerate formation or elevated NH3/NH+4 is essential only for the maintenance of the elevated levels of the messenger RNAs.

Interactions between adenosine and oscillatory cAMP signaling regulate size and pattern in Dictyostelium

We present evidence for the hypothesis that in multicellular structures of Dictyostelium, production of adenosine by hydrolysis of cAMP near the tip region prevents both generation of competing tips and differentiation of prespore cells near the tip, and thus establishes a "prestalk" region. We demonstrate that adenosine affects the immunological prespore specific staining pattern in slugs in a manner opposite to cAMP:cAMP induces an increase of prespore antigen; adenosine induces a decrease. When endogenous adenosine is removed from slugs, prespore vacuoles are synthesized throughout the prestalk region. Adenosine was found to inhibit the induction of prespore differentiation by cAMP in an apparently competitive manner. It was also found that adenosine specifically increased the amount of tissue controlled by one tip, probably by inhibiting generation of competing oscillators. Removing endogenous adenosine from slugs resulted in a decrease of tip dominance.