Host-virus transcriptome dynamics determined from microarray analyses

Cyanobacteria are highly abundant in the oceans and are constantly exposed to lytic viruses. The T4-like cyanomyoviruses are abundant in the marine environment and have broad host ranges relative to other cyanophages. It is currently unknown whether broad-host-range phages specifically tailor their infection program for each host, or employ the same program irrespective of the host infected. Also unknown is how different hosts respond to infection by the same phage. Here we used microarray and RNA-seq analyses to investigate the interaction between the Syn9 T4-like cyanophage and three phylogenetically, ecologically and genomically distinct marine Synechococcus strains: WH8102, WH7803 and WH8109. Strikingly, Syn9 led a nearly identical infection and transcriptional program in all three hosts. Different to previous assumptions for T4-like cyanophages, three temporally regulated gene expression classes were observed. Furthermore, a novel regulatory element controlled early gene transcription, and host-like promoters drove middle gene transcription, different to the regulatory paradigm for T4. Similar results were found for the P-TIM40 phage during infection of Prochlorococcus NATL2A. Moreover, genomic and metagenomic analyses indicate that these regulatory elements are abundant and conserved among T4-like cyanophages. In contrast to the near-identical transcriptional program employed by Syn9, host responses to infection involved host-specific genes primarily located in hypervariable genomic islands, substantiating islands as a major axis of phage-cyanobacteria interactions. Our findings suggest that the ability of broad host-range phages to infect multiple hosts is more likely dependent on the effectiveness of host defense strategies than on differential tailoring of the infection process by the phage. We investigated the transcriptional response of three Synechococcus strains (WH7803, WH8102 and WH8109) to infection by the Syn9 cyanophage as well as the transcriptional program of the Syn9 phage during infection of these three hosts. We further investigated the transcriptional program of the P-TIM40 cyanophage during infection of Prochlorococcus NATL2A and compared these to the results for the Syn9 cyanophage. For Syn9 infection of the three Synechococcus hosts, the dataset consisted of 121 microarray measurements from three biological replicates at different time points after phage addition (2-5 min and 0.5, 1, 1.5, 2, 3, 4 h) of infected and uninfected control cultures. This resulted in a total of 42, 39 and 40 microarrays for WH7803, WH8102, and WH8109, respectively. For P-TIM40 infection of Prochlorococcus NATL2A, four time points (0.5, 1, 2 and 3 h after infection) were analyzed from three biological replicates for a total of 12 microarray measurements. Custom-made Affymetrix microarrays (SYN-PHG) were used for this study.