Proteomic and Transcriptomic Profiling Identifies Early Developmentally Regulated Proteins in Dictyostelium Discoideum

Abstract

Cyclic AMP acts as a secondary messenger involving different cellular functions in eukaryotes. Here, proteomic and transcriptomic profiling has been combined to identify novel early developmentally regulated proteins in eukaryote cells. These proteomic and transcriptomic experiments were performed in Dictyostelium discoideum given the unique advantages that this organism offers as a eukaryotic model for cell motility and as a nonmammalian model of human disease. By comparing whole-cell proteome analysis of developed (cAMP-pulsed) wild-type AX2 cells and an independent transcriptomic analysis of developed wild-type AX4 cells, our results show that up to 70% of the identified proteins overlap in the two independent studies. Among them, we have found 26 proteins previously related to cAMP signaling and identified 110 novel proteins involved in calcium signaling, adhesion, actin cytoskeleton, the ubiquitin-proteasome pathway, metabolism, and proteins that previously lacked any annotation. Our study validates previous findings, mostly for the canonical cAMP-pathway, and also generates further insight into the complexity of the transcriptomic changes during early development. This article also compares proteomic data between parental and cells lacking glkA, a GSK-3 kinase implicated in substrate adhesion and chemotaxis in Dictyostelium. This analysis reveals a set of proteins that show differences in expression in the two strains as well as overlapping protein level changes independent of GlkA.

Sulfur sequestration promotes multicellularity during nutrient limitation

“…10a ), consistent with increased proteasome activity upon starvation (Extended Data Fig. 3f ) and with previous studies in cAMP-pulsed D. discoideum 34 .…”

Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes in Dictyostelium discoideum

“…For most of these isozymes, different functions and substrates could be identified. Taken together, this differentiation-dependent regulation seems to represent a general feature during the onset of multicellularity and cell differentiation for accurate development of the vegetative amoeba into a fruiting body [ 32 , 34 , 36 , 73 , 74 ].…”

“…A typical feature of these species is their adaptation to starving conditions by undergoing a developmental cycle that forms a multicellular organism with differentiated cell types [ 30 , 32 , 33 ]. This developmental cycle features a highly regulated program of alterations in protein expression, leading to the complex formation of a new organism [ 34 , 35 , 36 ]. Upon starvation, a cAMP signal is released, triggering aggregation and eventually the complex formation of fruiting bodies.…”

Mitochondrial Processes during Early Development of Dictyostelium discoideum: From Bioenergetic to Proteomic Studies

“…D. discoideum cells, during the early steps of aggregation when unicellular cells start to move and form waves, are referred to as early developmental stages induced by starvation ( Figure 1 ) [ 1 ]. These early developmental stages have been studied previously [ 7 , 8 ]. Accordingly, transcriptomic and cell proteomic data on mutant strains lacking genes that are crucial for cell aggregation are available [ 7 ].…”