Transcriptomic and Metabolomics Profiling of Phage–Host Interactions between Phage PaP1 and Pseudomonas aeruginosa

Abstract

The basic biology of bacteriophage–host interactions has attracted increasing attention due to a renewed interest in the therapeutic potential of bacteriophages. In addition, knowledge of the host pathways inhibited by phage may provide clues to novel drug targets. However, the effect of phage on bacterial gene expression and metabolism is still poorly understood. In this study, we tracked phage–host interactions by combining transcriptomic and metabolomic analyses in Pseudomonas aeruginosa infected with a lytic bacteriophage, PaP1. Compared with the uninfected host, 7.1% (399/5655) of the genes of the phage-infected host were differentially expressed genes (DEGs); of those, 354 DEGs were downregulated at the late infection phase. Many of the downregulated DEGs were found in amino acid and energy metabolism pathways. Using metabolomics approach, we then analyzed the changes in metabolite levels in the PaP1-infected host compared to un-infected controls. Thymidine was significantly increased in the host after PaP1 infection, results that were further supported by increased expression of a PaP1-encoded thymidylate synthase gene. Furthermore, the intracellular betaine concentration was drastically reduced, whereas choline increased, presumably due to downregulation of the choline–glycine betaine pathway. Interestingly, the choline–glycine betaine pathway is a potential antimicrobial target; previous studies have shown that betB inhibition results in the depletion of betaine and the accumulation of betaine aldehyde, the combination of which is toxic to P. aeruginosa. These results present a detailed description of an example of phage-directed metabolism in P. aeruginosa. Both phage-encoded auxiliary metabolic genes and phage-directed host gene expression may contribute to the metabolic changes observed in the host.

Phage-specific metabolic reprogramming of virocells

“…3; Dataset Table 7). This pattern contrasts with the more evenly distributed transcriptional response found in many other phage-host systems [28,31,32,[58][59][60]; though none of these studies involved siphoviruses. Whether this late transcriptomic response is a feature of HS2 or of siphoviruses in general-especially those suspected to integrate-is an open question, but it suggests that HS2 can largely utilize existing host resources to replicate itself.…”

Investigating Lactococcus lactis MG1363 Response to Phage p2 Infection at the Proteome Level

“…It was previously reported that the lactococcal phage c2 downregulated many host genes involved in amino acid and energy metabolism pathways, suggesting a global repression of energy-consuming functions (9). Similarly, the lytic phage PaP1 suppressed 85% of the differentially expressed P. aeruginosa genes, with most genes belonging to amino acid metabolism pathways (10). In B. subtilis, phage infection triggered the repression of genes involved in utilization of specific carbon sources (8).…”

“…In comparison, transcriptomic analysis of B. subtilis cells infected with phage 29 revealed significant changes in less than 2% of the host genes (8). Approximately 7% of P. aeruginosa genes were differentially expressed in phage-infected cells when compared with uninfected cells, most being downregulated in the late infection phase (10). In a culture of L. lactis IL1403 infected by phage c2, whole-genome microarrays detected 61 differentially expressed genes, corresponding to less than 3% of the annotated genes (9).…”

“…lactis IL1403 by the lytic siphophage c2 was studied with whole-genome microarrays (9). The effects of phage infection on gene expression were also studied through transcriptomic and metabolomic analysis of Pseudomonas aeruginosa cells infected with the lytic phage PaP1 (Myoviridae family) (10). Those reports provided insight into the control of gene expression during phage infection.…”

Bacteriophages Promote Metabolic Changes in Bacteria Biofilm

“…Moreover, since antibiotics have lost much of their power against bacteria, phage therapy may acquire a major role in combating resistant bacterial strains. Consequently, understanding the molecular determinants of phage-host interactions appears to be an essential step for a safe application of the therapy [14]. Recently, metabolomics analysis has suggested that the molecular response to phage infection is specific, as the molecular interactions taking place depend upon the phage and host bacterial strain [15,16].…”