Project description:Cyanobacteria are highly abundant in the oceans where they are constantly exposed to lytic viruses. Some viruses are restricted to a narrow host range while others infect a broad range of hosts. It is currently unknown whether broad-host range phages employ the same infection program, or regulate their program in a host-specific manner to accommodate for the different genetic makeup and defense systems of each host. Here we used a combination of microarray and RNA-seq analyses to investigate the interaction of three phylogentically distinct Synechococcus strains, WH7803, WH8102, and WH8109, with the broad-host range T4-like myovirus, Syn9, during infection. Strikingly, we found that the phage led a nearly identical expression program in the three hosts despite considerable differences in host gene content. On the other hand, host responses to infection involved mainly host-specific genes, suggesting variable attempts at defense against infection. A large number of responsive host genes were located in hypervariable genomic islands, substantiating genomic islands as a major axis of phage-bacteria interactions in cyanobacteria. Furthermore, transcriptome analyses and experimental determination of the complete phage promoter map revealed three temporally regulated modules and not two as previously thought for cyanophages. In contrast to T4, an extensive, previously unknown regulatory motif drives expression of early genes and host-like promoters drive middle-gene expression. These promoters are highly conserved among cyanophages and host-like middle promoters extend to other T4-like phages, indicating that the well-known mode of regulation in T4 is not the rule among the broad family of T4-like phages. We investigated the infection process and transcriptional program of the P-TIM40 cyanophage during infection of a Prochlorococcus NATL2A host. The results are discussed in conjunction with results obtained from the infection process for the Syn9 cyanophage in three different Synechococcus hosts: WH7803 (Dufresne et al. 2008), WH8102 (Palenik et al. 2003) and WH8109 (sequenced as part of this study).

Project description:Pf-5 is an important biocontrol strain of Pseudomonas fluorsecens, that improves plant growth, mainly via the production of secondary metabolites and growth/colonisation competition. Copper is a broad-spectrum antimicrobial that is effective against bacteria, fungi and even viruses in soluble forms such as copper sulfate and to a lesser extent in solid form, such as copper surfaces. Copper sulfate is commonly sprayed on food crops to increase yield and is becoming more routinely used due to the increasing problem of resistance to standard pesticides. Thus, an obvious question that remains is: what effect is this introduced copper having on these important biocontrol strains? First, the phenotypic effects of copper on carbon utilisation and pH tolerance was tested using Biolog. Interestingly, the ability of Pf-5 to utilise amino acids as a sole carbon source was largely unaltered, but the presence of copper completely eliminated the utilisation of carbohydrates or fatty acids, and diminished the use of carboxylic acids and amines. This could be explained by copper-mediated disruptions of enzymes in metabolic pathways, such as the TCA cycle. The effect on gene expression was examined using reverse transcriptomics, which established molecular bases for the phenotypic results, and confirmed some known mechanisms for copper resistance, efflux and transporter proteins, and highlighted the delicate interplay with cellular control of iron, as well as uncovered the interesting relationship between integrated bacteriophage and copper as a molecular switch. The integrated phage, Prophage 01, was downregulated in the presence of copper and when this phage was activated with Mitomycin C, the copper appeared to stop the phage from going into lytic cycle and protected lysis of the cells. Prophage 01 is integrated between the housekeeping genes mutS and cinA and is conserved throughout many Pseudomonas. However, only Pf-5, out of the 10 strains tested seemed to be protected from cell lysis by copper, indicating that Prophage 01 in Pf-5 has unique features that interact with Cu. Two-condition experiment, where normal culture in rich medium versus cell treated with CuSO4. 3 biological replicates including 3 technical replicates for one of the biological replicates and 2 technical replicates for another of biological replicates. Swap-dye experiments were performed.

Project description: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

Project description:Optimality of the spontaneous prophage induction rate. Cortes MG1, Krog J2, Balázsi G3. 1 Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA. 2 The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA. 3 Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA. Electronic address: gabor.balazsi@stonybrook.edu. Abstract Lysogens are bacterial cells that have survived after genomically incorporating the DNA of temperate bacteriophages infecting them. If an infection results in lysogeny, the lysogen continues to grow and divide normally, seemingly unaffected by the integrated viral genome known as a prophage. However, the prophage can still have an impact on the host's phenotype and overall fitness in certain environments. Additionally, the prophage within the lysogen can activate the lytic pathway via spontaneous prophage induction (SPI), killing the lysogen and releasing new progeny phages. These new phages can then lyse or lysogenize other susceptible nonlysogens, thereby impacting the competition between lysogens and nonlysogens. In a scenario with differing growth rates, it is not clear whether SPI would be beneficial or detrimental to the lysogens since it kills the host cell but also attacks nonlysogenic competitors, either lysing or lysogenizing them. Here we study the evolutionary dynamics of a mixture of lysogens and nonlysogens and derive general conditions on SPI rates for lysogens to displace nonlysogens. We show that there exists an optimal SPI rate for bacteriophage λ and explain why it is so low. We also investigate the impact of stochasticity and conclude that even at low cell numbers SPI can still provide an advantage to the lysogens. These results corroborate recent experimental studies showing that lower SPI rates are advantageous for phage-phage competition, and establish theoretical bounds on the SPI rate in terms of ecological and environmental variables associated with lysogens having a competitive advantage over their nonlysogenic counterparts. Copyright © 2019 The Author(s). Published by Elsevier Ltd.. All rights reserved.

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