Genome-Wide Expression Dynamics of a Marine Virus and its Host during Lytic Infection

We used microarray analysis to investigate whole genome transcriptome dynamics of the marine cyanobacterium Prochlorococcus sp. strain MED4 and the T7-like podovirus P-SSP7 over a time course during the 8 hour latent period of lytic infection prior to cell lysis. Manuscript Summary: Interactions between bacterial hosts and their viruses (phages) lead to reciprocal genome evolution through a dynamic co-evolutionary process1-5. Phage-mediated transfer of host genes – often located in genome islands – has had a major impact on microbial evolution1, 4, 6. Furthermore, phage genomes have clearly been shaped by the acquisition of genes from their hosts2, 3, 5. Here we investigate whole-genome expression of a host and phage, the marine cyanobacterium Prochlorococcus and a T7-like cyanophage during lytic infection, to gain insight into these co-evolutionary processes. While most of the phage genome was linearly transcribed over the course of infection, 4 phage-encoded bacterial metabolism genes were part of the same expression cluster, even though they are physically separated on the genome. These genes — encoding photosystem II D1 (psbA), high-light inducible protein (hli), transaldolase (talC) and ribonucleotide reductase (nrd) — are transcribed together with phage DNA replication genes and appear to make up a functional unit involved in energy and deoxynucleotide production needed for phage replication in resource-poor oceans. Also unique to this system was the upregulation of numerous genes in the host during infection. These may be host stress response genes, and/or genes induced by the phage. Many of these host genes are located in genome islands and have homologues in cyanophage genomes. We hypothesize that phage have evolved to utilize upregulated host genes, leading to their stable incorporation into phage genomes and their subsequent transfer back to hosts in genome islands. Thus activation of host genes during infection may be directing the co-evolution of gene content in both host and phage genomes. Keywords: time course, viral infection, marine cyanobacteria, podovirus, bacteriophage, stress response Triplicate independent cultures of the cyanobacterium Prochlorococcus MED4 were grown as described in the protocols section below. Each of the three cultures was divided into two subcultures. One subculture for each culture was infected with phage and the other subculture served as the paired uninfected control. Infection Treatment: The T7-like podovirus P-SSP7 was added to Prochlorococcus MED4 at a ratio of 3 infective phage per 1 cyanobacterial cell. Samples were taken for transcriptome analysis every hour after addition of phage during the 8 h latent period of infection: at 0, 1, 2, 3, 4, 5, 6, 7, 8 h after infection for a total of 9 samples per infected biological replicate. Control Treatment: Paired control (uninfected) cells were amended with filter-sterilized spent medium and samples taken at 0, 1, 2, 3, 4, 8 h after addition for a total of 6 samples per “uninfected” biological replicate. A total of 45 samples were analyzed - 27 infected samples from 3 biological replicates and 18 uninfected (control) samples from 3 biological replicates. Series 1, 2, 3 - infected cells; Series 4, 5, 6 - uninfected control cells. Paired infected and uninfected treatments: The paired treatments are: Series 1 and 4; 2 and 5; 3 and 6.