Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA139137 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:HU is a conserved prokaryotic nucleoid-associated protein known for its role in DNA binding and maintaining negative supercoils in DNA. HU also binds to a few RNAs but the natural targets are unknown. To understand the biology of HU interactions with RNA in Escherichia coli, potential HU-RNA in vivo complexes were immunoprecipitated and bound RNAs were examined by hybridization to whole-genome tiling arrays. We observed HU associations with rRNA, multiple tRNAs, a few sRNAs and a small, distinct set of mRNAs. More importantly, we also identified associations between HU and ten intragenic non-coding (nonc) RNAs, two of which are homologous to the annotated Bacterial Interspersed Mosaic Elements (BIME) and boxC elements; the other eight RNAs have not been annotated. We confirmed binding of HU to BIME RNA in vitro. Since HU and some unidentified RNAs have been implicated in the nucleoid structure, we explored an idea that HU, along with some or all of the nonc RNA species discovered here bind to BIME and/or boxC repeats to condense chromosomal DNA in a specific fashion. We propose that nonc RNAs may interact with both HU and DNA repeats to form ternary complexes, which are the anchoring points separating different chromosomal domains.
2012-12-07 | GSE28565 | GEO
Project description:The physiological role of the various nucleoid-associated proteins in bacteria and HU in particular has been addressed in a number of studies but remains so far not fully understood. In this work, a genome-wide microarray hybridization approach, combined with in vivo genetic experimentation, has been performed in order to compare and evaluate the effect of HUalpha, HUbeta and HUalphabeta on the transcription of the Escherichia coli K12 genes as a function of growth phase. The histone-like protein HU is present in the E. coli cell under three dimeric forms (HUalphabeta, HUalpha2 and HUbeta2) in a ratio that varies with growth phase. The experimental protocol is designed to handle strain genotype and growth phase as independent variables. Keywords: genotype, growth phase
2009-01-01 | GSE11183 | GEO
Project description:To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, ‘histone-like’ protein (i.e. Fis, IHF and H-NS) binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci.
2013-05-01 | GSE40304 | GEO
Project description:Nucleoid remodeling facilitated by DNA supercoiling results in changes in nucleoid configuration and involves nucleoid-associated proteins (NAPs) and structural maintenance of chromosomes (SMC) proteins among others. Changes in nucleoid configurations regulated by NAPs are synchronized with cellular adaptation and influence the simultaneous expression of several genes. HU, a ubiquitous bacterial histone-like protein, is among the most conserved and abundant NAPs in eubacteria. In Escherichia coli, HU forms dimers by HUα self-association (HUαα) or by HUα-HUβ interactions (HUαβ). HUα is mostly expressed during lag and early exponential growth phase and HUβ is expressed only during the later exponential and stationary phase, pointing to distinct HUαα/DNA and HUαβ/DNA packaging of the nucleoid in regulating expression patterns during growth and stasis. Mutations or the deletion of HU transform the E. coli nucleoid to a different form and alter overall transcription program; thus, HU interactions with DNA directly affect global gene regulation. Recently, analysis of high-resolution contact maps of the E. coli nucleoid revealed an important role of HU to promote long-range DNA-DNA contacts within the nucleoid. Yet, the molecular connections between HU-DNA interactions and changes in nucleoid architecture that regulate gene expression globally remain unknown. Here, we explored the higher-order E. coli nucleoid organization by soft x-ray tomography (SXT) and revealed an effect of HU surface charges in overall nucleoid organization and rearrangements. We also studied global transcription by next-generation RNA sequencing (RNA-Seq) and found a link between nucleoid rearrangement and changes in global transcription. To determine the functional relationships of observed nucleoid rearrangement and HU-DNA interactions, we also characterized the overall organization of HU nucleoprotein complexes in solution by small angle x-ray scattering (SAXS). We found that HUαα-mediated DNA networks are different at different ionic strengths and pHs. By means of macromolecular crystallography, we additionally elucidate HUαα dependent molecular switches that modulate DNA networking. This integrative structural study explains how HUαα regulates dynamic transformations of the nucleoid by DNA bridging to control nucleoid rearrangement and global gene regulation.
2020-04-01 | GSE134667 | GEO
Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.
| 2230352 | ecrin-mdr-crc
Project description:Dps is the most abundant nucleoid-associated protein in starved Escherichia coli with ∼180000 copies per cell. Dps binds DNA and oxidizes iron, facilitating survival in harsh environments. Dps–DNA complexes can form crystalline structures, leading to the proposed model that Dps reorganizes the starved E. coli nucleoid into a compact liquid crystal, slowing chromosome dynamics, and limiting access of other proteins to DNA. In this work, we directly tested this model using live-cell super-resolution microscopy and Hi-C analysis. We found that after 96 h of starvation, Dps compacts the nucleoid, and increases short-range DNA–DNA interactions but does not affect chromosome accessibility to large protein nanocages or small restriction enzymes. We also report that chromosome dynamics and organization are primarily impacted by the bacterial growth phase; the effect of Dps is relatively minor. Our work clarifies the role of Dps in modulating nucleoid properties, and we propose an updated model for Dps–DNA interactions in which Dps binds, protects, and compacts DNA largely without influencing chromosome access, dynamics, and organization. Additionally, this work provides a general framework for assessing the impact of nucleoid-associated proteins on key aspects of chromosome function in live cells.
2026-01-06 | GSE293552 | GEO
Project description:To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, ‘histone-like’ protein (i.e. Fis, IHF and H-NS) binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci. A 4 chips study of exponentially growing wild type E. coli strain MG1655 grown in LB rich media or after induction of the stringent response by serine hydroxamate for 30 min. Two technical replicates, Three biological replicates mixed prior hybridization on the chip.
2013-05-01 | E-GEOD-40304 | biostudies-arrayexpress
Project description:The Escherichia coli nucleoid is confined within a rod shaped cell many times smaller than the outstretched chromosome. While extensive compaction is necessary for this process, the chromosome must at the same time remain accessible to essential cellular processes such as replication and transcription. Currently, the individual contributions of cellular confinement, chromosome topology, replication and transcription on nucleoid organization are not well understood. Here we synchronize E. coli cells in stationary phase, where replication has ceased, each cell contains only one copy of the chromosome, and transcription is minimal. We then release the cells and capture chromosome contacts and transcription immediately following release and through-out one cell cycle. Polymer models of confined and topologically constrained circular polymers revealed that cellular confinement and topology do not contribute extensively to the organization of the E. coli nucleoid. Rather, local nucleoid structure is established concurrent with replication, and higher order organization is formed by the replication dependant clustering of linearly distant SeqA bound sites and cell cycle specific gene transcription.
2017-12-25 | GSE87117 | GEO
Project description:HupA is a nucleoid associated protein, homologic to E. coli HU protein. Its binding is affected by DNA supercoiling. ChIP-seq experiment goal was to analyze changing of HupA binding in the strain with depleted levels of TopA (high supercoling) vs strain with normal level of TopA.
2022-12-01 | E-MTAB-11369 | biostudies-arrayexpress
Project description:The Escherichia coli nucleoid is confined within a rod shaped cell many times smaller than the outstretched chromosome. While extensive compaction is necessary for this process, the chromosome must at the same time remain accessible to essential cellular processes such as replication and transcription. Currently, the individual contributions of cellular confinement, chromosome topology, replication and transcription on nucleoid organization are not well understood. Here we synchronize E. coli cells in stationary phase, where replication has ceased, each cell contains only one copy of the chromosome, and transcription is minimal. We then release the cells and capture chromosome contacts and transcription immediately following release and through-out one cell cycle. Polymer models of confined and topologically constrained circular polymers revealed that cellular confinement and topology do not contribute extensively to the organization of the E. coli nucleoid. Rather, local nucleoid structure is established concurrent with replication, and higher order organization is formed by the replication dependant clustering of linearly distant SeqA bound sites and cell cycle specific gene transcription.
2017-12-25 | GSE87071 | GEO