Meta-Analysis of Immune Induced Gene Expression Changes in Diverse Drosophila melanogaster Innate Immune Responses

Abstract

Organisms are commonly infected by a diverse array of pathogens and mount functionally distinct responses to each of these varied immune challenges. Host immune responses are characterized by the induction of gene expression, however, the extent to which expression changes are shared among responses to distinct pathogens is largely unknown. To examine this, we performed meta-analysis of gene expression data collected from Drosophila melanogaster following infection with a wide array of pathogens. We identified 62 genes that are significantly induced by infection. While many of these infection-induced genes encode known immune response factors, we also identified 21 genes that have not been previously associated with host immunity. Examination of the upstream flanking sequences of the infection-induced genes lead to the identification of two conserved enhancer sites. These sites correspond to conserved binding sites for GATA and nuclear factor κB (NFκB) family transcription factors and are associated with higher levels of transcript induction. We further identified 31 genes with predicted functions in metabolism and organismal development that are significantly downregulated following infection by diverse pathogens. Our study identifies conserved gene expression changes in Drosophila melanogaster following infection with varied pathogens, and transcription factor families that may regulate this immune induction.

Keywords: Drosophila melanogaster; gene expression; innate immunity; pathogen infection; transcriptome analysis.

Figure 1

Chromosomal location of altered genes. Each identified gene has been mapped to its chromosomal location, indicated by its position on each chromosome arm of the Drosophila melanogaster genome (A–E). For each panel, the x axis represents the genomic position, inverted cyan triangles indicate the positions of induced genes and the magenta triangles indicate the positions of downregulated genes.

Figure 2

Gene ontology analysis of infection induced genes. The log₂ fold enrichment for selected GO terms. The Biological Process (BP) category is shown in cyan, and the Cellular Component (CC) category is shown in magenta. See Table S3. for complete GO term analysis of induced genes.

Figure 3

Motifs associated with infection induced genes. De novo motif finding identified 3 motifs (Motifs 1–3) that are enriched in the upstream sequences of the induced genes. The consensus motifs are represented as sequence logos (A–C, top). Motif matching identifies Motif 1 as being significantly similar to the GATAe binding site (A). Motif 2 shows significant similarity to the dl binding site (B). (D–F) Box-whisker plots showing the distribution of rank-products for induced genes with and without the indicated motifs. A lower rank-product is indicative of higher expression levels. (D) Induced genes with Motif 1 in the upstream region have significantly lower rank-products. (E) The presence of Motif 2 does not impact the rank-product distribution. (F) Induced genes with both motifs have significantly lower rank-products. Asterisk (*) indicates p < 0.05 relative to induced genes without the indicated motif.

Figure 4

Gene ontology analysis of downregulated genes. The log₂ fold enrichment for selected GO terms. The Biological Process (BP) category is shown in cyan, the Molecular Function (MF) category is shown in yellow, and the Cellular Component (CC) category is shown in magenta. See Table S5 for complete GO term analysis of downregulated genes.

Figure 5

Motif associated with downregulated genes. De novo motif finding identified 1 motif (Motif D1) that is enriched in the upstream sequences of the induced genes. The consensus motif is represented as a sequence logo (A, top). Motif matching identifies Motif D1 as being significantly similar to the Hr3 binding site (A). (B) Box-whisker plot showing the distribution of rank-products for the downregulated genes with and without Motif D1. The presence of Motif D1 does not impact the rank-product distribution.