Article

Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium

Department of Clinical and Biological Sciences, University of Turin, Ospedale S, Luigi, 10043 Orbassano, Torino, Italy.
BMC Genomics (Impact Factor: 4.04). 02/2008; 9(1):291. DOI: 10.1186/1471-2164-9-291
Source: PubMed

ABSTRACT Phagocytosis plays a major role in the defense of higher organisms against microbial infection and provides also the basis for antigen processing in the immune response. Cells of the model organism Dictyostelium are professional phagocytes that exploit phagocytosis of bacteria as the preferred way to ingest food, besides killing pathogens. We have investigated Dictyostelium differential gene expression during phagocytosis of non-pathogenic bacteria, using DNA microarrays, in order to identify molecular functions and novel genes involved in phagocytosis.
The gene expression profiles of cells incubated for a brief time with bacteria were compared with cells either incubated in axenic medium or growing on bacteria. Transcriptional changes during exponential growth in axenic medium or on bacteria were also compared. We recognized 443 and 59 genes that are differentially regulated by phagocytosis or by the different growth conditions (growth on bacteria vs. axenic medium), respectively, and 102 genes regulated by both processes. Roughly one third of the genes are up-regulated compared to macropinocytosis and axenic growth. Functional annotation of differentially regulated genes with different tools revealed that phagocytosis induces profound changes in carbohydrate, amino acid and lipid metabolism, and in cytoskeletal components. Genes regulating translation and mitochondrial biogenesis are mostly up-regulated. Genes involved in sterol biosynthesis are selectively up-regulated, suggesting a shift in membrane lipid composition linked to phagocytosis. Very few changes were detected in genes required for vesicle fission/fusion, indicating that the intracellular traffic machinery is mostly in common between phagocytosis and macropinocytosis. A few putative receptors, including GPCR family 3 proteins, scaffolding and adhesion proteins, components of signal transduction and transcription factors have been identified, which could be part of a signalling complex regulating phagocytosis and adaptational downstream responses.
The results highlight differences between phagocytosis and macropinocytosis, and provide the basis for targeted functional analysis of new candidate genes and for comparison studies with transcriptomes during infection with pathogenic bacteria.

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    • "On the other hand, when confronted with non-pathogenic bacteria such as non-virulent Klebsiella pneumoniae or Bacillus subtilis, Dictyostelium cells use specific molecular mechanisms to kill different bacteria (Benghezal et al., 2006; Lelong et al., 2011). In addition, large-scale transcriptional studies point to differential metabolic and signalling pathways being activated when Dictyostelium cells are grown in different sources of bacteria (Sillo et al., 2008; Nasser et al., 2013). It is thus likely that Dictyostelium recognizes various kinds of bacteria and adapts its physiology. "
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    ABSTRACT: Recognition of bacteria by metazoans is mediated by receptors that recognize different types of microorganisms and elicit specific cellular responses. The soil amoebae Dictyostelium discoideum feeds upon a variable mixture of environmental bacteria, and it is expected to recognize and adapt to various food sources. To date, however, no bacteria-sensing mechanisms have been described. In this study, we isolated a Dictyostelium mutant (fspA KO) unable to grow in the presence of non-capsulated Klebsiella pneumoniae bacteria, but growing as efficiently as wild-type cells in the presence of other bacteria, such as Bacillus subtilis. FspA KO cells were also unable to respond to K. pneumoniae and more specifically to bacterially secreted folate in a chemokinetic assay, while they responded readily to B. subtilis. Remarkably, both WT and fspA KO cells were able to grow in the presence of capsulated LM21 K. pneumoniae, and responded to purified capsule, indicating that capsule recognition may represent an alternative, FspA-independent mechanism for K. pneumoniae sensing. When LM21 capsule synthesis genes were deleted, growth and chemokinetic response were lost for fspA KO cells, but not for WT cells. Altogether, these results indicate that Dictyostelium amoebae use specific recognition mechanisms to respond to different K. pneumoniae elements.
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    • "Under laboratory conditions, the cells are able to graze on a very large variety of Gram-negative and Gram-positive bacteria, including different species of Enterobacter, Serratia, Salmonella, Yersinia, Proteus, Aeromonas, Alcaligenes, Acinetobacter, Staphylococcus, Listeria, and Bacillus (Depraitere and Darmon, 1978). They are also capable of modulating their response to different types of bacteria by activating specific sets of gene transcripts (Farbrother et al., 2006; Carilla-Latorre et al., 2008; Sillo et al., 2008, 2011). In a recent paper, (Nasser et al., 2013) have studied global transcriptional response of wild type and selected mutant cells to a series of Gram-negative and Gram-positive bacteria, and they could show that cells respond differently to these two large families of bacteria. "
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