Bacteriophage short-term in situ evolution: what can we learn from comparative analysis of the ecologically linked phage isolates.


Andrey Letarov1, 2, Alla Golomidova1, Nickolai Prokhorov1, Sergey Nazarov4, Peter Leiman4, Vladislav Babenko5, Yuri Knirel3, Eugene Kulikov1, 2, Pavel Ivanov1, et al.

1Winogradsky Institute of Microbiology, RC Biotechnology RAS, Moscow, Russia
2Moscow Istitute of Physics and Technology, Dolgoprudny, Russia
3N.D. Zelinsky Institute of Organic Chemistry RAS, Moscow, Russia
4Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
5SRI of Physical-chemical Medicine FMBA RF, Moscow, Russia


The remarkable ability of the bacteriophages to adapt to the variable ecological situations is undoubtedly one of the key features of these viruses lifestyle. It is widely believed that the main mechanism of this adaptation relies on short-term (co)evolution processes. Phage evolution has been extensively studied using the model laboratory microcosms. A large body of information also comes from the comparison of the phage isolates and/or phage genomes of unknown or random origin. Here we use in-depth genomic and experimental comparative analysis of the series of highly related and ecologically linked coliphage isolates. We studied a set of the N4-like G7C-related podoviruses isolated in 2006-2013 from the horse faeces sampled from a single animal population. Our data indicate that in contrast to the in vitro co-evolving phage G7C – E.coli 4s system, where the evolutionary adaptations were driven predominantly by point mutations, the impact of the genetic exchange of the phage(s) with the available genetic pool of the community plays a very significant role in shaping of the viral genomes in an open and complex natural microbial community. We detected several types of the modular exchange events, including homing nucleases mobility, mobile type I introns invasions, swapping of the fragments of the receptor recognition proteins and else. The interpretation of these observations is based on the extensive experimental study of G7C phage biology encompassing the detailed adsorption apparatus characterization including RBPs X-ray crystallography, virion Cryo-EM reconstruction and biochemical analysis of the enzymatic activity of the tailspikes, the intron activity confirmation and else. Our conclusions are in agreement with the results of analysis of the set of T5-like isolates obtained from the same location. So one can conclude that the evolutionary trajectories of phage genomes are determined not only by the environmental conditions but also by the composition of the local community metagenome.






Reference:
Posters Day 2-T03-Pos-20
Session:
Posters Covering Ecology, Host population control, Co-Evolutionary dynamics and Subversion/Evasion of Host Defences
Presenters:
Andrey Letarov
Session:
Day 2 Posters Covering: Ecology, Host population control, Co-evolutionary dynamics and Subversion/Evasion of host defences
Presentation type:
Poster presentation
Room:
Poster Halls
Date:
Tuesday, 19 July 2016
Time:
12:05 - 15:00