Zlatohurska M. Structural and functional organization of the genomes of temperate phages 49 and 59 Erwinia horticola

The dissertation is devoted to the study of structural and functional genome organization of temperate phages 49 and 59 as well as phage-phage and phage-bacterial interactions within the phytopathogenic Erwinia horticola system, the causative agent of beech black bacteriosis in Ukraine Comparative genomic analysis has shown that temperate phages 49 and 59 are unique as their genomes reveal no significant similarity to that of any previously reported viruses of Enterobacteriaceae. At the same time, phages 49 and 59 share extensive nucleotide sequence identity across the regions encoding capsid assembly, DNA packaging, and lysis. The overall nucleotide sequence similarity of the two genomes was 47%. The revealed synteny and gene order indicate phages 49 and 59 as the novel members of the lambdoid phage group. Due to the availability of whole-genome sequence data, the information on virion DNA of phages 49 and 59 has been refined and supplemented. Its properties were studied using the standard restriction and bioinformatic analyses. It has been shown that the virion DNA of both phages are permuted. Phage 59 is characterized by circular permutation, while phage 49 has discrete permutation. The virion DNA of phage 59 contains an abnormal cleavage sites that are not hydrolyzed by KpnI restriction enzyme. It was shown that the pool of phage 59 obtained on the mutant auxotrophic strain E. horticola 450 His3 represents the heterogeneous population consisting of two phage variants that differ in capsid diameter. Both phage variants package the virion DNA molecules of about the same size and have similar protein contents, but the relative quantitative content of several their major structural proteins is different. It was found that the interaction between phage 49 and resident prophage in the E. horticola 450(59) lysogenic culture is characterized by the development of abortive infection. The phage exclusion is expressed in reduced plating efficiency and phage progeny release. The obtained data suggest that the current phage-bacterial system develops abortive response affecting virion morphogenesis of phage 49. It was established that the release of two temperate phages 49 and 59 occurs as a result of interaction between E. horticola cells and the phage tail-like macromolecular carotovoricins of Pectobacterium carotovorum, as well as Escherichia coli phages T2 and T4. Interpreting the literature data and our findings, the hypothetical model of new phenomenon named phage mediated phage induction was proposed. The origin of temperate phages 49 and 59 was reviewed: they should be considered as E. horticola phages, rather than those of P. сarotovorum.