Extracellular DNA controls expression ofPseudomonas aeruginosagenes involved in nutrient utilization, metal homeostasis, acid pH tolerance, and virulence

Abstract

ABSTRACTPseudomonas aeruginosagrows in extracellular DNA-enriched biofilms and infection sites. Extracellular DNA (eDNA) is generally considered a structural biofilm polymer required for aggregation and biofilm maturation. In addition, eDNA can sequester divalent metal cations, acidify the growth media, and serve as a nutrient source. Here we determine the transcriptome of planktonicP. aeruginosagrown in the presence of eDNA using RNA-seq. Transcriptome analysis identified 89 induced genes and 76 repressed genes in the presence of eDNA (FDR<0.05), and transcriptionalluxfusions were used to confirm eDNA regulation. A large number of eDNA-induced genes appear to be involved in utilizing DNA as a nutrient. Several eDNA-induced genes are also induced by acidic pH 5.5, and growth in the presence of eDNA or acidic pH promoted an acid tolerance response inP. aeruginosa. ThecyoABCDEterminal oxidase is induced at pH 5.5 and contributed to the acid tolerance phenotype. Quantitative metal analysis confirmed that DNA binds to diverse metals, which helps explain why many genes involved in a general uptake of metals were controlled by eDNA. Growth in the presence of eDNA also promoted intracellular bacterial survival and influenced virulence and during the acute infection model of fruit flies. The diverse functions of the eDNA-regulated genes underscore the important role of this extracellular polymer in promoting antibiotic resistance, virulence, acid tolerance, and nutrient utilization; phenotypes that contribute to long-term survival.