The near‐atomic resolution cryo electron microscopy structure of the lactococcal siphophage 1358 virion mature full capsid

Abstract

Lactococcus lactis, a Gram(+) lactic acid‐producing bacterium used for the manufacture of several fermented dairy products, is subject to infection by diverse virulent tailed phages, leading to industrial fermentation failures. Despite the availability of several antiphage measures, new phages keep emerging in this ecosystem. This constant viral risk has led to a sustained interest in the study of their biology, diversity, and evolution. Lactococcal phages now constitute a wide ensemble of at least 10 distinct genotypes within the Caudovirales order, many of them belonging to the Siphoviridae family. Lactococcal siphophage 1358, currently the only member of its group, displays a noticeably high genomic similarity to some Listeria phages as well as a host range limited to a few L. lactis strains. These genomic and functional characteristics stimulated our interest in this phage. Here, we report the near‐atomic resolution cryo electron microscopy (cryo‐EM) structure of the 1358 virion mature full capsid. Recent advances in cryo‐EM have enabled structure determination of macromolecular complexes at near‐atomic resolution. However, structure determination and atomic modelling still remains a challenging task susceptible to model bias and overfitting especially while using de novo methods. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution cryo‐EM structure allowing to complement the previously published complete structural picture of a unique lactococcal phage at lower resolution and have deeper insight into structural organization of it's capsid.