טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentFedida Ayalla
SubjectIdentification and Characterization of Genes Involved in
the Response of Marine Cyanobacteria to Viral
Infection
DepartmentDepartment of Biology
Supervisor Professor Debbie Lindell
Full Thesis textFull thesis text - English Version


Abstract

The unicellular cyanobacteria of the genera Synechococcus and Prochlorococcus are highly abundant in the oceans, playing a major role in primary production. They are constantly exposed to infection by phages which are thought to have a major impact on their population dynamics and evolution. However, no known defense mechanisms against bacteriophages have been identified in these cyanobacteria. The aim of this study was to explore the interaction between a single T4-like myovirus, Syn9, and three Synechococcus strains (WH8102, WH7803 and WH8109) in order to define and compare the phage infection process and transcriptional program and to identify and characterize host genes that respond to infection. We found that the phage infection process and transcriptional program were almost identical in all three hosts. Different to previous assumptions for T4-like cyanophages, three temporal gene expression clusters were detected. Furthermore, a novel promoter motif and host-like promoters were identified upstream of early and middle phage genes, respectively, different to the regulatory paradigm for T4. However, the late gene promoter motif was similar to that for T4 late genes. Similar results were found for the P-TIM40 phage during infection of Prochlorococcus NATL2A.

The response of the three distinct hosts to Syn9 infection showed a common general transcriptional pattern: while the transcript level of most genes (> 90%) had declined by about 0.5 h after infection, there was a small group of genes whose transcript level increased during infection. Some showed a transient increase immediately upon infection while others increased later during infection. Additionally, in all hosts there was small group of genes (~ 1%) whose transcript level remained unchanged during the phage latent period. In sharp contrast to the nearly identical phage transcriptional program these host response genes (increased or unchanged) were mainly strain specific. Nonetheless, some belonged to common functional groups such as cell envelope, carbon fixation, DNA repair, respiration and nutrient utilization. In addition, the response genes were primarily located in hypervariable genomic islands in all three hosts, supporting the hypothesis that these islands play an important role in interactions between cyanobacteria and their phages.

Host response genes may constitute a host attempt at defense against phage infection or be induced by the phage for its own needs. Toward testing these hypotheses we inactivated two WH8102 response genes that contain host defense-related domains: SYNW1659, containing a DUF3387 domain that is associated with restriction enzymes; and SYN1946, containing a PhoH ATPase domain and a PIN domain mostly found in toxin-antitoxin operons. Phage virulence and the length of the infection cycle were similar to the wild-type in both mutants. In contrast, phage genomic replication and the yield of infective phages were significantly lower in the DUF3387 mutant and significantly higher in the PIN-PhoH mutant. These results suggest that the first gene aids phage production while the second plays a role in restraining the infection process. Thus it appears that some host response genes are utilized by the phage for improved infection while others function in an attempt at defense against the phage.