Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

Abstract

Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organised at various length scales. This has implications on modulating (when not enabling) the core biological processes of replication, transcription, segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. We also discuss some attempts of interpretation that unify different results, highlighting the role that statistical and soft condensed matter physics, and in particular classic and more modern tools from the theory of polymers, plays in describing this system of fundamental biological importance, and pointing to possible directions for future investigation.

30 pages, accepted for publication in Reports on Progress in Physics

References in corpus (9)

• Random Time-Scale Invariant Diffusion and Transport Coefficients
• Probing microscopic origins of confined subdiffusion by first-passage observables
• Thermodynamic pathways to genome spatial organization in the cell nucleus
• Fractional Langevin Equation: Over-Damped, Under-Damped and Critical Behaviors
• Spatial and topological organization of DNA chains induced by gene co-localization
• The collapse transition of randomly branched polymers -renormalized field theory
• Gene clusters reflecting macrodomain structure respond to nucleoid perturbations
• Mass Fractal Dimension of the Ribosome and Implication of its Dynamic Characteristics
• A thermodynamic model for agglomeration of DNA-looping proteins

Cited by in corpus (16)

• From a melt of rings to chromosome territories: The role of topological constraints in genome folding
• Folding and cytoplasm viscoelasticity contribute jointly to chromosome dynamics
• Simulating the Entropic Collapse of Coarse-Grained Chromosomes
• DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling
• Segregative phase separation scenario of the formation of the bacterial nucleoid
• Preferential localization of the bacterial nucleoid
• Bacterial nucleoid: Interplay of DNA demixing and supercoiling
• Organization of the bacterial nucleoid by DNA-bridging proteins and globular crowders
• Looping and Clustering model for the organization of protein-DNA complexes on the bacterial genome
• Entropic elasticity and dynamics of the bacterial chromosome: a simulation study
• Requirements for DNA-bridging proteins to act as topological barriers of the bacterial genome
• Free energy and segregation dynamics of two channel-confined polymers of different length
• Bacterial chromosome organization I: crucial role of release of topological constraints and molecular crowders
• Intermittent transport of bacterial chromosomal loci
• Tethered Particle Motion Technique in Crowded Media: Compaction of DNA by Globular Macromolecules
• Peano modes at the D=2 delocalization transition