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Nucleoid associated proteins and their effect on E. coli chromosome

https://doi.org/10.1101/2020.11.05.369934
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/j.1460-2075.1991.tb07935.xopenalex-snapshot
The new gene mukB codes for a 177 kd protein with coiled‐coil domains involved in chromosome partitioning of E. coli.
inferredcites →https://doi.org/10.1002/jcc.21787openalex-snapshot
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
inferredcites →https://doi.org/10.1006/jmbi.1996.0068openalex-snapshot
Histone-like Protein HU and Bacterial DNA Topology: Suppression of an HU Deficiency by Gyrase Mutations
inferredcites →https://doi.org/10.1006/jmbi.1997.1310openalex-snapshot
Variation in HU composition during growth of Escherichia coli: the heterodimer is required for long term survival
inferredcites →https://doi.org/10.1006/jmbi.1998.2160openalex-snapshot
A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome 1 1Edited by R. Ebright
inferredcites →https://doi.org/10.1007/bf00328479openalex-snapshot
Electron microscopy of membrane-free folded chromosomes from Escherichia coli
inferredcites →https://doi.org/10.1016/0022-2836(72)90342-7openalex-snapshot
On the structure of the folded chromosome of Escherichia coli
inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot
VMD: Visual molecular dynamics
inferredcites →https://doi.org/10.1016/0923-2508(91)90029-aopenalex-snapshot
Mutants defective in chromosome partitioning in E. coli
inferredcites →https://doi.org/10.1016/j.bbagrm.2012.02.012openalex-snapshot
Architectural organization in E. coli nucleoid
inferredcites →https://doi.org/10.1016/j.bpj.2011.04.030openalex-snapshot
Entropy-Based Mechanism of Ribosome-Nucleoid Segregation in E. coli Cells
inferredcites →https://doi.org/10.1016/j.cell.2008.08.031openalex-snapshot
The MatP/matS Site-Specific System Organizes the Terminus Region of the E. coli Chromosome into a Macrodomain
inferredcites →https://doi.org/10.1016/j.cell.2017.12.027openalex-snapshot
Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins
inferredcites →https://doi.org/10.1016/j.jmb.2006.09.043openalex-snapshot
Mechanism of Chromosome Compaction and Looping by the Escherichia coli Nucleoid Protein Fis
inferredcites →https://doi.org/10.1016/j.jsb.2006.05.006openalex-snapshot
The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective
inferredcites →https://doi.org/10.1016/j.molcel.2012.09.009openalex-snapshot
Molecular Basis for a Protein-Mediated DNA-Bridging Mechanism that Functions in Condensation of the E. coli Chromosome
inferredcites →https://doi.org/10.1016/s0021-9258(18)66770-5openalex-snapshot
Purification and properties of the Escherichia coli host factor required for inversion of the G segment in bacteriophage Mu.
inferredcites →https://doi.org/10.1038/ncomms10466openalex-snapshot
MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation
inferredcites →https://doi.org/10.1038/s41576-019-0185-4openalex-snapshot
Chromosome organization in bacteria: mechanistic insights into genome structure and function
inferredcites →https://doi.org/10.1038/sj.emboj.7600434openalex-snapshot
Macrodomain organization of the Escherichia coli chromosome
inferredcites →https://doi.org/10.1046/j.1365-2443.2000.00350.xopenalex-snapshot
Two types of localization of the DNA‐binding proteins within the Escherichia coli nucleoid
inferredcites →https://doi.org/10.1063/1.2374884openalex-snapshot
A Monte Carlo simulation study of branched polymers
inferredcites →https://doi.org/10.1073/pnas.0308230101openalex-snapshot
Dual architectural roles of HU: Formation of flexible hinges and rigid filaments
inferredcites →https://doi.org/10.1073/pnas.0611686104openalex-snapshot
Spiral structure of Escherichia coli HUαβ provides foundation for DNA supercoiling
inferredcites →https://doi.org/10.1073/pnas.68.1.6openalex-snapshot
The Folded Genome of Escherichia coli Isolated in a Protein-DNA-RNA Complex
inferredcites →https://doi.org/10.1073/pnas.72.9.3428openalex-snapshot
Characterization of a novel, low-molecular-weight DNA-binding protein from Escherichia coli.
inferredcites →https://doi.org/10.1074/jbc.274.46.33105openalex-snapshot
Twelve Species of the Nucleoid-associated Protein from Escherichia coli
inferredcites →https://doi.org/10.1088/1478-3975/5/4/046001openalex-snapshot
Timing the start of division in E. coli : a single-cell study
inferredcites →https://doi.org/10.1093/nar/29.24.5107openalex-snapshot
An architectural role of the Escherichia coli chromatin protein FIS in organising DNA
inferredcites →https://doi.org/10.1101/2020.06.29.178194openalex-snapshot
Mapping the Multiscale Organisation of Escherichia Coli Chromosome in a Hi-C-integrated Model
inferredcites →https://doi.org/10.1101/cshperspect.a000349openalex-snapshot
Bacterial Chromosome Organization and Segregation
inferredcites →https://doi.org/10.1101/gad.14.2.212openalex-snapshot
Dynamic organization of chromosomal DNA in Escherichia coli
inferredcites →https://doi.org/10.1101/gad.290312.116openalex-snapshot
Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus
inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot
Matplotlib: A 2D Graphics Environment
inferredcites →https://doi.org/10.1111/j.1365-2958.2005.04799.xopenalex-snapshot
A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure
inferredcites →https://doi.org/10.1111/j.1365-2958.2008.06239.xopenalex-snapshot
DNA dynamics vary according to macrodomain topography in the E. coli chromosome
inferredcites →https://doi.org/10.1128/jb.00957-12openalex-snapshot
The Escherichia coli SMC Complex, MukBEF, Shapes Nucleoid Organization Independently of DNA Replication
inferredcites →https://doi.org/10.1128/jb.181.20.6361-6370.1999openalex-snapshot
Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid
inferredcites →https://doi.org/10.1128/mmbr.58.2.211-232.1994openalex-snapshot
The bacterial nucleoid revisited
inferredcites →https://doi.org/10.1146/annurev-genet-110711-155421openalex-snapshot
Chromosome Replication and Segregation in Bacteria
inferredcites →https://doi.org/10.1159/000369099openalex-snapshot
MukBEF, a Chromosomal Organizer
inferredcites →https://doi.org/10.1371/journal.pgen.1008456openalex-snapshot
Architecture of the Escherichia coli nucleoid
inferredcites →https://doi.org/10.25080/majora-629e541a-00eopenalex-snapshot
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations
inferredcites →https://doi.org/10.3389/fmicb.2018.02019openalex-snapshot
Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes
inferredcites →https://doi.org/10.4014/jmb.1309.09072openalex-snapshot
Protective Effects of Probiotic Lactobacillus rhamnosus IMC501 in Mice Treated with PhIP

What points at this work

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inferred← citeshttps://doi.org/10.1016/j.bpj.2022.03.002openalex-snapshot
Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1013898openalex-snapshot
Abundant positively-charged proteins underlie JCVI-Syn3A’s expanded nucleoid and ribosome distribution
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