Next-Generation “-omics” Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa

Abstract

As interest in the therapeutic and biotechnological potentials of bacteriophages has grown, so has value in understanding their basic biology. However, detailed knowledge of infection cycles has been limited to a small number of model bacteriophages, mostly infecting Escherichia coli. We present here the first analysis coupling data obtained from global next-generation approaches, RNA-Sequencing and metabolomics, to characterize interactions between the virulent bacteriophage PAK_P3 and its host Pseudomonas aeruginosa. We detected a dramatic global depletion of bacterial transcripts coupled with their replacement by viral RNAs over the course of infection, eventually leading to drastic changes in pyrimidine metabolism. This process relies on host machinery hijacking as suggested by the strong up-regulation of one bacterial operon involved in RNA processing. Moreover, we found that RNA-based regulation plays a central role in PAK_P3 lifecycle as antisense transcripts are produced mainly during the early stage of infection and viral small non coding RNAs are massively expressed at the end of infection. This work highlights the prominent role of RNA metabolism in the infection strategy of a bacteriophage belonging to a new characterized sub-family of viruses with promising therapeutic potential.

Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell

“…This is also the case for the bacteriophages presented in this work. In the interest of pointing out the significance of the described genes and their effect during the infection, relative expression levels of both bacterial and bacteriophagic genes were studied ( Figure 5 ; Supplementary Data Sheet S2; Supplementary Table S1), where the viral relative transcript levels outnumbered the host’s, as expected (Chevallereau et al, 2016). Apart from the nicotinamide mononucleotide adenyltransferase ( NMNAT ; ALP47012 for φ Grn1 and ALP47393 for φ St2), an enzyme present in both phages and the host, φ Grn1 and φ St2 also possess a nicotinamide phosphoribosyltransferase ( NAMPT ; ALP46980 for φ Grn1 and ALP47363 for φ St2), which is absent from V. alginolyticus and is able to utilize nicotinamide as a substrate and convert it to nicotinamide d-ribonucleotide, making a shortcut in the NAD + biosynthesis pathway.…”

“…The presence of multiple ATP-dependent enzymes could indicate a high ATP demand during the lytic cycle. Direct evidence of increased accumulation of ATP during phage infection has been recently provided by Chevallereau et al (2016; Supplementary Table S3). Additionally in our case, at least 97 genomes of 250,485 bp have to be synthetized during phage infection, which could dictate even higher nucleotide metabolic demand and subsequently energy in the form of ATP.…”

Phage therapy: awakening a sleeping giant

“…Tailed phages infect bacteria and hijack several cellular systems to produce progeny virions before being released by rupturing the cell. This can all happen within minutes after initial contact [11]. By differing in mode of action to static antibiotic drugs, most therapeutic phages are not only effective against antibiotic-sensitive and antibiotic-resistant bacteria, when co-applied they are often a synergistic therapy [16].…”

“…For the past three decades, a considerable amount of knowledge has been gained with regard to the genetic, structural, functional, and ecological features of phages, for examples [10][11][12]. Accordingly, the progression in the development of phage therapies has grown steadily across a wide variety of diseases (Table 1).…”

Cross-Regulation between Bacteria and Phages at a Posttranscriptional Level

“…Unconventional types of gene regulation might also be employed by sRNA1 and sRNA2, which are expressed from the genome of the PAK_P3 phage infecting Pseudomonas aeruginosa (83). Both sRNAs accumulate as ~100 nucleotide transcripts and are differentially regulated during the infection process, with expression peaking during late stages of infection.…”