Xenogeneic silencing and bacterial genome evolution: mechanisms for DNA recognition imply multifaceted roles of xenogeneic silencers

B Duan, P Ding, WW Navarre, J Liu… - Molecular Biology and …, 2021 - academic.oup.com
Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the
deleterious effects due to the unregulated expression of newly acquired foreign genes …

High-resolution, genome-wide mapping of positive supercoiling in chromosomes

MS Guo, R Kawamura, ML Littlehale, JF Marko… - Elife, 2021 - elifesciences.org
Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-
dimensional organization of chromosomes. However, there are currently no methods to …

Variable DNA topology is an epigenetic generator of physiological heterogeneity in bacterial populations

CJ Dorman - Molecular Microbiology, 2023 - Wiley Online Library
Transcription is a noisy and stochastic process that produces sibling‐to‐sibling variations in
physiology across a population of genetically identical cells. This pattern of diversity reflects …

Regulators of rDNA array morphology in fission yeast

AJ Cockrell, JJ Lange, C Wood, M Mattingly… - Plos …, 2024 - journals.plos.org
Nucleolar morphology is a well-established indicator of ribosome biogenesis activity that
has served as the foundation of many screens investigating ribosome production. Missing …

Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression

CM Hustmyer, R Landick - Molecular Microbiology, 2024 - Wiley Online Library
DNA in bacterial chromosomes is organized into higher‐order structures by DNA‐binding
proteins called nucleoid‐associated proteins (NAPs) or bacterial chromatin proteins (BCPs) …

Rok from B. subtilis: Bridging genome structure and transcription regulation

AM Erkelens, B van Erp, WJJ Meijer… - Molecular …, 2024 - Wiley Online Library
Bacterial genomes are folded and organized into compact yet dynamic structures, called
nucleoids. Nucleoid orchestration involves many factors at multiple length scales, such as …

GapR binds DNA through dynamic opening of its tetrameric interface

Q Huang, B Duan, X Dong, S Fan… - Nucleic Acids Research, 2020 - academic.oup.com
GapR is a nucleoid-associated protein that is an essential regulator of chromosome
replication in the cell cycle model Caulobacter crescentus. Here, we demonstrate that free …

The DNA recognition motif of GapR has an intrinsic DNA binding preference towards AT-rich DNA

Q Huang, B Duan, Z Qu, S Fan, B Xia - Molecules, 2021 - mdpi.com
The nucleoid-associated protein GapR found in Caulobacter crescent us is crucial for DNA
replication, transcription, and cell division. Associated with overtwisted DNA in front of …

ATAC-seq reveals megabase-scale domains of a bacterial nucleoid

MD Melfi, K Lasker, X Zhou, L Shapiro - bioRxiv, 2021 - biorxiv.org
Here we adapted ATAC-seq to probe chromosome accessibility of bacterial cells. We found
that the chromosome of Caulobacter crescentus is composed of eight differentially …

Changes in Higher-Order Chromosomal Structure of Klebsiella pneumoniae Under Simulated Microgravity

Y Wang, W Shen, M Yin, W Huang, B Ye, P Li… - Frontiers in …, 2022 - frontiersin.org
Our previous work have shown that certain subpopulations of Klebsiella pneumoniae exhibit
significant phenotypic changes under simulated microgravity (SMG), including enhanced …