In vivo crystallization of bacterial nucleoid under stress. Possibilities of study at X-ray free electron lasers

TL;DR

This paper explores the potential of X-ray free electron lasers (XFELs) to study the nanocrystalline structure of bacterial nucleoids formed under stress, aiming to clarify DNA conformation within these complexes.

Contribution

It discusses experimental configurations and challenges for using XFELs to determine DNA structure in bacterial nanocrystals formed during stress conditions.

Findings

XFELs can potentially reveal detailed DNA conformations in bacterial nanocrystals.

The study outlines specific experimental approaches for in vivo and in vitro samples.

Challenges include sample size and stability during XFEL experiments.

Abstract

Under prolonged starvation, the nucleoid of E. coli bacteria forms nanocrystalline complexes with the protein Dps. By one hypothesis, this effect is considered to be a manifestation of a general strategy of self-preservation of living organisms under adverse conditions by forming stable ordered structures which do not require consumption of energy for maintaining the order. The effect of nucleoid biocrystallization in starved bacteria has been investigated in a number of studies using electron microscopy. However, this method did not answer all questions regarding the structure of the nanocrystals, and, primarily, the question of the true conformation of DNA in these complexes. This issue is particularly important because it is related to a more general, actively researched topic of organization of the genetic material, which affects gene expression and is thus critical for the functioning of organisms. The intracellular DNA-Dps nanocrystals have the size in the range of hundreds of nanometers and are thus particularly suitable for study at X-ray free electron lasers (XFELs). In this paper, we discuss the possible configurations of XFEL experiments aimed at determining the conformation of DNA in the DNA-Dps nanocrystals grown in vivo and in vitro, as well as the specific features and challenges associated with this type of sample. We conclude that the XFEL technique has a high potential for uncovering the structural details of bacterial nucleoid restructuring under stress.