Abstract
Dictyostelium discoideum amoebae feed by ingesting bacteria, then killing them in phagosomes. Ingestion and killing of different bacteria have been shown to rely on largely different molecular mechanisms. One would thus expect that D. discoideum adapts its ingestion and killing machinery when encountering different bacteria. In this study, we investigated by RNA sequencing if and how D. discoideum amoebae respond to the presence of different bacteria by modifying their gene expression patterns. Each bacterial species analyzed induced a specific modification of the transcriptome. Bacteria such as Bacillus subtilis, Klebsiella pneumoniae, or Mycobacterium marinum induced a specific and different transcriptional response, while Micrococcus luteus did not trigger a significant gene regulation. Although folate has been proposed to be one of the key molecules secreted by bacteria and recognized by hunting amoebae, it elicited a very specific and restricted transcriptional signature, distinct from that triggered by any bacteria analyzed here. Our results indicate that D. discoideum amoebae respond in a highly specific, almost non-overlapping manner to different species of bacteria. We additionally identify specific sets of genes that can be used as reporters of the response of D. discoideum to different bacteria.
Highlights
Dictyostelium discoideum is a free-living amoeba, and a well-established model organism for the study of basic aspects of differentiation, signal transduction, phagocytosis, cytokinesis and cell motility (Cosson and Lima, 2014; Nichols et al, 2015; Dunn et al, 2017)
In order to measure changes in gene expression when D. discoideum encounters different bacteria, we incubated D. discoideum in HL5c medium, or in HL5c medium supplemented with live bacteria or with 1 mM folate
No extracellular bacteria growth was observed after 4 h of coculture with D. discoideum cells (Supplementary Figure S1A)
Summary
Dictyostelium discoideum is a free-living amoeba, and a well-established model organism for the study of basic aspects of differentiation, signal transduction, phagocytosis, cytokinesis and cell motility (Cosson and Lima, 2014; Nichols et al, 2015; Dunn et al, 2017). Several transcriptomic studies have revealed that specific metabolic and signaling pathways are upregulated when D. discoideum cells feed on different bacteria (Farbrother et al, 2006; Carilla-Latorre et al, 2008; Sillo et al, 2008; Nasser et al, 2013). This specific modulation probably reflects at least in part the fact that each bacterial species contains different nutrients. This study identified sets of genes that can be used to test whether specific D. discoideum mutants respond to various stimuli
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