Architectural organization in E. coli nucleoid

Abstract

In contrast to organized hierarchical structure of eukaryotic chromosome, bacterial chromosomes are believed not to have such structures. The genomes of bacteria are condensed into a compact structure called the nucleoid. Among many architectural, histone-like proteins which associate with the chromosomal DNA is HU which is implicated in folding DNA into a compact structure by bending and wrapping DNA. Unlike the majority of other histone-like proteins, HU is highly conserved in eubacteria and unique in its ability to bind RNA. Furthermore, an HU mutation profoundly alters the cellular transcription profile and consequently has global effects on physiology and the lifestyle of E. coli. Here we provide a short overview of the mechanisms by which the nucleoid is organized into different topological domains. We propose that HU is a major player in creating domain-specific superhelicities and thus influences the transcription profile from the constituent promoters. This article is part of a Special Issue entitled: Chromatin in time and space.

A stochastic reaction-diffusion model for protein aggregation on DNA

“…In this limit, the ground state is described by a single pitch spiral as observed experimentally. 6,8,11,12 The coexistence of left-and right-handed spiral¯laments in equilibrium, as reported previously, 12 is also predicted by the model [see Fig. 4(b)].…”

“…6,8,11,12 In that sense, this study will be di®erent from the traditional works on XY models carried out in the thermodynamic limit i.e. N P !…”

“…6,8,11,12 Here, this property is a consequence of the repulsive electrostatic interaction between the HU proteins, which forces them to reorganize around the backbone. Monte Carlo simulations on a¯nite system of 15 proteins identi¯ed three di®erent ground state regimes [see Fig.…”

“…10 Interestingly, HU¯laments tend to form spiral con¯gurations that excite supercoiling, which could potentially promote DNA compaction and regulate the promoter activity. 6,8,11,12 Atomistic simulation is the most accurate method to study protein-DNA complexes. However, the high complexity of the interactions and the huge number of atoms involved make atomistic simulations infeasible even with powerful supercomputers.…”

Persistent super-diffusive motion of Escherichia coli chromosomal loci

“…The cytosol is a highly crowded environment, which promotes the chromosome to be (semi-)collapsed due to osmotic self-attraction 9,10 . However, in vivo the compacted chromosome (nucleoid) maintains a well-defined shape and tends to occupy a significantly smaller volume than the cell, likely a result of the activity of numerous DNA-associated proteins with varying functionality [11][12][13][14] . The average mobility of loci is a function of chromosomal coordinate, suggesting spatially varying physical organization and/or noise levels due to transcription, translation or protein activity 4 .…”