A MicroRNA Network Controls <i>Legionella pneumophila</i> Replication in Human Macrophages via LGALS8 and MX1

Abstract

<i>Legionella pneumophila</i> is an important cause of pneumonia. It invades alveolar macrophages and manipulates the immune response by interfering with signaling pathways and gene transcription to support its own replication. MicroRNAs (miRNAs) are critical posttranscriptional regulators of gene expression and are involved in defense against bacterial infections. Several pathogens have been shown to exploit the host miRNA machinery to their advantage. We therefore hypothesize that macrophage miRNAs exert positive or negative control over <i>Legionella</i> intracellular replication. We found significant regulation of 85 miRNAs in human macrophages upon <i>L. pneumophila</i> infection. Chromatin immunoprecipitation and sequencing revealed concordant changes of histone acetylation at the putative promoters. Interestingly, a trio of miRNAs (miR-125b, miR-221, and miR-579) was found to significantly affect intracellular <i>L. pneumophila</i> replication in a cooperative manner. Using proteome-analysis, we pinpointed this effect to a concerted downregulation of galectin-8 (LGALS8), DExD/H-box helicase 58 (DDX58), tumor protein P53 (TP53), and then MX dynamin-like GTPase 1 (MX1) by the three miRNAs. In summary, our results demonstrate a new miRNA-controlled immune network restricting <i>Legionella</i> replication in human macrophages.<b>IMPORTANCE</b> Cases of <i>Legionella pneumophila</i> pneumonia occur worldwide, with potentially fatal outcome. When causing human disease, <i>Legionella</i> injects a plethora of virulence factors to reprogram macrophages to circumvent immune defense and create a replication niche. By analyzing <i>Legionella</i>-induced changes in miRNA expression and genomewide chromatin modifications in primary human macrophages, we identified a cell-autonomous immune network restricting <i>Legionella</i> growth. This network comprises three miRNAs governing expression of the cytosolic RNA receptor DDX58/RIG-I, the tumor suppressor TP53, the antibacterial effector LGALS8, and MX1, which has been described as an antiviral factor. Our findings for the first time link TP53, LGALS8, DDX58, and MX1 in one miRNA-regulated network and integrate them into a functional node in the defense against <i>L. pneumophila</i>.