scholarly journals Confinement and crowding control the morphology and dynamics of a model bacterial chromosome

Soft Matter ◽  
2019 ◽  
Vol 15 (12) ◽  
pp. 2677-2687 ◽  
Author(s):  
Pinaki Swain ◽  
Bela M. Mulder ◽  
Debasish Chaudhuri
Keyword(s):  
Bacterial Chromosome ◽  
Cylindrical Cell ◽  
Bacterial Chromosomes

Motivated by recent experiments probing the shape, size and dynamics of bacterial chromosomes in growing cells, we consider a circular polymer attached to side-loops to model the chromosome confined to a cylindrical cell, in the presence of cytoplasmic crowders.

scholarly journals Mesoscale Simulation of Bacterial Chromosome and Cytoplasmic Nanoparticles in Confinement

Entropy ◽  
2021 ◽  
Vol 23 (5) ◽  
pp. 542
Author(s):  
Shi Yu ◽  
Jiaxin Wu ◽  
Xianliang Meng ◽  
Ruizhi Chu ◽  
Xiao Li ◽  
...  
Keyword(s):  
Cell Wall ◽  
Bacterial Chromosome ◽  
Dynamic Simulations ◽  
External Compression ◽  
Langevin Dynamic ◽  
Bacterial Chromosomes ◽  
Metabolic Reactions ◽  
Non Gaussian ◽  
Chromosome Segments ◽  
Cytoplasmic Particle

In this study we investigated, using a simple polymer model of bacterial chromosome, the subdiffusive behaviors of both cytoplasmic particles and various loci in different cell wall confinements. Non-Gaussian subdiffusion of cytoplasmic particles as well as loci were obtained in our Langevin dynamic simulations, which agrees with fluorescence microscope observations. The effects of cytoplasmic particle size, locus position, confinement geometry, and density on motions of particles and loci were examined systematically. It is demonstrated that the cytoplasmic subdiffusion can largely be attributed to the mechanical properties of bacterial chromosomes rather than the viscoelasticity of cytoplasm. Due to the randomly positioned bacterial chromosome segments, the surrounding environment for both particle and loci is heterogeneous. Therefore, the exponent characterizing the subdiffusion of cytoplasmic particle/loci as well as Laplace displacement distributions of particle/loci can be reproduced by this simple model. Nevertheless, this bacterial chromosome model cannot explain the different responses of cytoplasmic particles and loci to external compression exerted on the bacterial cell wall, which suggests that the nonequilibrium activity, e.g., metabolic reactions, play an important role in cytoplasmic subdiffusion.

scholarly journals Structure of bacterial chromosome: An analysis of DNA-protein interactions in vivo

2017 ◽  
Vol 71 (0) ◽  
pp. 0-0
Author(s):  
Joanna Hołówka ◽  
Małgorzata Płachetka
Keyword(s):  
Protein Interactions ◽  
Global Scale ◽  
Hierarchical Organization ◽  
Bacterial Chromosome ◽  
Precise Analysis ◽  
Bacterial Chromosomes ◽  
High Throughput Dna Sequencing ◽  
In Vivo Footprinting ◽  
Microscopy Techniques

According to recent reports, bacterial chromosomes exhibit a hierarchical organization. The number of proteins that bind DNA are responsible for local and global organization of the DNA ensuring proper chromosome compaction. Advanced molecular biology techniques combined with high-throughput DNA sequencing methods allow a precise analysis of bacterial chromosome structures on a local and global scale. Methods such as in vivo footprinting and ChIP-seq allow to map binding sites of analyzed proteins in certain chromosomal regions or along the whole chromosome while analysis of the spatial interactions on global scale could be performed by 3C techniques. Additional insight into complex structures created by chromosome-organizing proteins is provided by high-resolution fluorescence microscopy techniques.

scholarly journals circHiC: circular visualization of Hi-C data and integration of genomic data

2020 ◽  
Author(s):  
Ivan Junier ◽  
Nelle Varoquaux
Keyword(s):  
Genomic Data ◽  
Bacterial Chromosome ◽  
Link Type ◽  
Genome Wide ◽  
Bacterial Chromosomes ◽  
Wide Contact ◽  
Linear Chromosomes

SummaryGenome wide contact frequencies obtained using Hi-C-like experiments have raised novel challenges in terms of visualization and rationalization of chromosome structuring phenomena. In bacteria, display of Hi-C data should be congruent with the circularity of chromosomes. However, standard representations under the form of square matrices or horizontal bands are not adapted to periodic conditions as those imposed by (most) bacterial chromosomes. Here, we fill this gap and propose a Python library, built upon the widely used Matplotlib library, to display Hi-C data in circular strips, together with the possibility to overlay genomic data. The proposed tools are light and fast, aiming to facilitate the exploration and understanding of bacterial chromosome structuring data. The library further includes the possibility to handle linear chromosomes, providing a fresh way to display and explore eukaryotic data.Availability and implementationThe package runs under Python 3 and is freely available at https://github.com/TrEE-TIMC/circHiC. The documentation can be found at https://tree-timc.github.io/circhic/; images obtained in different organisms are provided in the gallery section and are accompanied with [email protected], [email protected]

Evolution of a strong electrovortex flow in a cylindrical cell

2020 ◽  
Vol 5 (12) ◽  
Author(s):  
Ilya Kolesnichenko ◽  
Peter Frick ◽  
Vladislav Eltishchev ◽  
Sergei Mandrykin ◽  
Frank Stefani
Keyword(s):  
Cylindrical Cell

scholarly journals Ability of a bacterial chromosome segment to invert is dictated by included material rather than flanking sequence.

Genetics ◽  
1991 ◽  
Vol 129 (4) ◽  
pp. 1021-1032 ◽  
Author(s):  
M J Mahan ◽  
J R Roth
Keyword(s):  
Homologous Recombination ◽  
Parent Strain ◽  
Genetic Material ◽  
Chromosomal Inversion ◽  
Chromosome Segment ◽  
Bacterial Chromosome ◽  
Flanking Sequence ◽  
Flanking Sequences ◽  
Almost All

Abstract Homologous recombination between sequences present in inverse order within the same chromosome can result in inversion formation. We have previously shown that inverse order sequences at some sites (permissive) recombine to generate the expected inversion; no inversions are found when the same inverse order sequences flank other (nonpermissive) regions of the chromosome. In hopes of defining how permissive and nonpermissive intervals are determined, we have constructed a strain that carries a large chromosomal inversion. Using this inversion mutant as the parent strain, we have determined the "permissivity" of a series of chromosomal sites for secondary inversions. For the set of intervals tested, permissivity seems to be dictated by the nature of the genetic material present within the chromosomal interval being tested rather than the flanking sequences or orientation of this material in the chromosome. Almost all permissive intervals include the origin or terminus of replication. We suggest that the rules for recovery of inversions reflect mechanistic restrictions on the occurrence of inversions rather than lethal consequences of the completed rearrangement.

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