Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum

Abstract

BackgroundDevelopment 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.ResultsHere, 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1491-7) contains supplementary material, which is available to authorized users.

The GATA transcription factor gene gtaG is required for terminal differentiation in Dictyostelium

“…2A compares the transcriptional phenotypes of the wild type and the gtaG − mutant. At early stages of development, the transcriptomes of the two strains are nearly indistinguishablethere is almost no distance between the gtaG − and the wild-type points at 0-8 h. It is also noticeable that the 0-h and 4-h samples cluster together, and there is a big distance between them and the 8-h sample, consistent with the finding that the biggest transcriptional transition in D. discoideum development occurs during the transition from single cells to multicellular behavior (Van Driessche et al, 2002;Parikh et al, 2010;Rosengarten et al, 2015). The distances between the two strains at 12 and 16 h are also rather small.…”

“…Examination of the developmental transcriptome has revealed vast changes in gene expression that occur in bursts during different developmental stages (Rosengarten et al, 2015). The most prominent change in gene expression coincides with the transition from unicellularity to multicellularity, at around 8-10 h of development.…”

Wild Dictyostelium discoideum social amoebae show plastic responses to the presence of nonrelatives during multicellular development

“…We calculated these pairwise distances between our samples and each of Rosengarten's time points in two different ways: once using all genes that were expressed in both experiments and a second time using only those genes that were reported as significantly differentially expressed by time (Rosengarten et al, ). We tried the second method in case it is more sensitive to any signal from the smaller number of genes that were informative for developmental progression.…”

“…We considered two previous hypotheses with opposite predictions: (a) cells in chimeras race to become spores (Kuzdzal‐Fick, Queller, & Strassmann, ) and (b) discoordination due to mixing two genotypes slows down development (Hirose et al, ). We compared the gene expression patterns of our samples to a developmental time series from the axenic laboratory strain AX4 (Rosengarten et al, ) and tested whether there was a consistent difference by social condition that may hint toward a relative acceleration or delay in development in chimeras.…”

Coenzyme A and protein CoAlation levels are regulated in response to oxidative stress and during morphogenesis in Dictyostelium discoideum

“…The expression of several thousand genes governs the programme of morphogenesis [25,26]. In this study we report the transcriptional regulation of genes involved in CoA biosynthesis during the life cycle of D. discoideum .…”