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.
Overall design: We investigated the transcriptional program of the Syn9 cyanophage during infection of three Synechococcus hosts (strains WH7803, WH8102 and WH8109) at different times after infection using whole transcriptome RNA sequence libraries. Four time points (5 min and 0.5, 1 and 2 h after infection) from two biological replicates of each of the three hosts were analyzed for a total of 24 samples. Pooled replicates of one of the infected Synechococcus hosts from 3 time points (0.5, 1 and 2 h after infection) were used for bisulfite strand-specific libraries (for a total of 3 samples). For 5?-end sequencing, Tobacco Acid Pyrophosphatase (TAP) treated libraries were prepared from two biological replicates for time points 0.5, 1 and 2 h after infection for a total of 18 samples. Untreated libraries were similarly prepared for one replicate of each infected host for a total of 9 libraries. All RNA-sequencing libraries were sequenced using the Illumina HiSeq platform at the Weizmann Institute.
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