RNA-Sequencing Reveals the Progression of Phage-Host Interactions between φR1-37 and Yersinia enterocolitica - PubMed (original) (raw)

RNA-Sequencing Reveals the Progression of Phage-Host Interactions between φR1-37 and Yersinia enterocolitica

Katarzyna Leskinen et al. Viruses. 2016.

Abstract

Despite the expanding interest in bacterial viruses (bacteriophages), insights into the intracellular development of bacteriophage and its impact on bacterial physiology are still scarce. Here we investigate during lytic infection the whole-genome transcription of the giant phage vB_YecM_φR1-37 (φR1-37) and its host, the gastroenteritis causing bacterium Yersinia enterocolitica. RNA sequencing reveals that the gene expression of φR1-37 does not follow a pattern typical observed in other lytic bacteriophages, as only selected genes could be classified as typically early, middle or late genes. The majority of the genes appear to be expressed constitutively throughout infection. Additionally, our study demonstrates that transcription occurs mainly from the positive strand, while the negative strand encodes only genes with low to medium expression levels. Interestingly, we also detected the presence of antisense RNA species, as well as one non-coding intragenic RNA species. Gene expression in the phage-infected cell is characterized by the broad replacement of host transcripts with phage transcripts. However, the host response in the late phase of infection was also characterized by up-regulation of several specific bacterial gene products known to be involved in stress response and membrane stability, including the Cpx pathway regulators, ATP-binding cassette (ABC) transporters, phage- and cold-shock proteins.

Keywords: Yersinia enterocolitica; bacteriophage; transcriptome; φR1-37.

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Figures

Figure 1

Figure 1

Growth curves of YeO3-R1 bacteria at different temperatures when infected with phage φR1-37. Bacteria infected with phage φR1-37 at MOIs of 10−1 to 10−5 were grown in LB at 4 °C (A), 10 °C (B), 16 °C (C), 22 °C (D), and 37 °C (E). Each data point in the graphs represents the average of eight replicates. The error bars represent the standard deviation for the optical density calculated for each time point. Note the different axis scales in the different panels.

Figure 2

Figure 2

Percentage of RNA sequencing reads aligning to the φR1-37 phage genome at different time points post-infection.

Figure 3

Figure 3

The progression of φR1-37 genome transcription during the infection cycle. The number of reads aligning to every 250 bp fragment of both strands of the phage genome was plotted for each time point (A). The intensity of the color of the curves from grey to black indicate the consecutive time points (for high resolution image of Panel A, see Figure S4). Different temporal classes of φR1-37 gene expression (B). For each gene and infection phase the highest Total Gene Reads (TGR) value was set to 100% and the other values set accordingly. The genes were grouped into four temporal classes and the curves represent the averages calculated for these.

Figure 4

Figure 4

The change in the expression of the bacterial genes during the phage φR1-37 infection cycle. The early phase values represent the average data calculated for the 2 and 5 min time points, and the late phase values, the average for the 28, 35, 42 and 49 min time points. Shown are the Log2FC values between the early phase and the negative control (A), between the late phase and negative control (B), and between the late and early phases (C). Each dot represents the Log2FC value calculated for each gene separately. In the A, B and C graphs, the dots are ordered according to their gene location in the YeO3-R1 genome (the consecutive gene numbers on the X-axis are indicated with the scale at the bottom). The grey lines indicate the selected differential expression threshold of ±1.5. Panels D, E and F demonstrate that in the early phase most differentially expressed host genes are repressed (D), while in the late phase many differentially expressed host genes are activated (E) and this is even more pronounced when the late phase genes are compared to early phase genes (F). For panels D, E and F, the genes are arranged along the X-axis according to their decreasing log2FC values.

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