Mechanisms of bacteriophage assembly and ejection ,structure of condensed genome ( structure analysis )

Author: Tsotne Dvali
Keywords: bacteriophages, infection, assembly, phages
Annotation:

Abstract Bacteriophages , phages (Greek .φάγος - ‘absorption’) are virus selectively destroying bacterial cells. Their influence on Ecosystem and evolution is immense. Around 4000 bacteriophages are studied in relation with ~ 100 bacterias. In this work, studied bacteriophages are from: Myoviridae, Siphoviridae and Podoviridae families, with different specificities. From using available experimental data,I analysed every step of bacteriophage life cycle: assembly, packaging and ejection / infection. Assembly is a very complex process, similar to ejection and incorporation of phage DNA in the bacterial genome. I found significant correlation between ejection background processes and expression patterns.During packaging capsid is expanding ( 12-25% / increasing volume by ~50%) which is connected to inter-strand spacing ( standard / outer of 2.8-2.5 nm ). Goal of this work is to present multiple suggested models and analysis of processes involved in the assembly, packaging and infection. From multiple sources and available experimental data bases, decision was made to focus on few very important bacteriophages - T4, SPP1, P22 , T7 ( T-even(s),λ, φ29,HK97 ...etc.), their importance is consequence of shared traits and characteristics with related and unrelated phages of same and different groups, super families and even types ( eukaryotic viruses ). Majority of analysed phages are tailed and double stranded, but even in those frames, diversity differences between associated individuals are significant. There are few very important questions about dimensions, limitations, involved forces of the capsid. According to few experiments and simulation results on DNA ( ds ) packaging module, was established a general models of condensation, symmetry and mechanism of working element ( motor complex ), but because mismatches and simplifications of involved components, mainly water, counterions, DNA helices ( their sections with different or changed properties in different conditions and environment ) and internal proteins (including capsomer i.surfaces), in contrast with new advances create new questions . Important aspect of this work is partial deconstruction of mechanisms controlling the system and fluidity, range of mutations and alterations in those processes and what they produce. Analysis from energetical and structural standpoint allowed me to suggest a few schemes of processing and interaction models , involved in every captured step of bacteriophage ‘life cycle’, including effects of repulsive and attractive interactions of ds DNA in different local conditions, with and without environmental modification.

Lecture files:

ბაქტერიოფაგთა აწყობისა და გენომის ეჟექციის მექანიზმები, კონდენსირებული გენომის სტრუქტურის ანალიზი და ორ ჯაჭვიანი დნმ-ის მოდელები ფაგებში. [ka]