ArticleProceedings of the National Academy of Sciences of the United States of America2012
Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers, 1 of them a synthesis that pooled it.
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Who cites it
124 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Data integration through proximity-based networks provides biological principles of organization across scales.The Plant cell · 2013Pooled it
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- Prokaryotic homeostasis - a solution to thrive and survive.Frontiers in molecular biosciences · 2025Review
- Oligonucleotide library assisted sequence mining reveals promoter sequences with distinct temporal expression dynamics for applications inSynthetic biology (Oxford, England) · 2025Article
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- Stress-induced nucleoid remodeling in Deinococcus radiodurans is associated with major changes in Heat Unstable (HU) protein dynamics.Nucleic acids research · 2024Article
- Chromosomal Position of Ribosomal Protein Genes Affects Long-Term Evolution of Vibrio cholerae.mBio · 2023Article
- DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes.Nucleic acids research · 2023Article
- Pangenome-level analysis of nucleoid-associated proteins in theFrontiers in microbiology · 2023Article
- The role of replication-induced chromosomal copy numbers in spatio-temporal gene regulation and evolutionary chromosome plasticity.Frontiers in microbiology · 2023Article
- Variable DNA topology is an epigenetic generator of physiological heterogeneity in bacterial populations.Molecular microbiology · 2023Review
- Escherichia coli cell factories with altered chromosomal replication scenarios exhibit accelerated growth and rapid biomass production.Microbial cell factories · 2022Article
- Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization-A Timing Chain for the Bacterial Growth Cycle?Biomolecules · 2022Review
- Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription.Nucleic acids research · 2022Article
- Evolution of Complex Regulation for Cell-Cycle Control.Genome biology and evolution · 2022Article
- Relationship between the Chromosome Structural Dynamics and Gene Expression-A Chicken and Egg Dilemma?Microorganisms · 2022Review
- Reciprocally rewiring and repositioning the Integration Host Factor (IHF) subunit genes inMicrobial genomics · 2022Article
- The bacterial promoter spacer modulates promoter strength and timing by length, TG-motifs and DNA supercoiling sensitivity.Scientific reports · 2021Article
64 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In Escherichia coli crosstalk between DNA supercoiling, nucleoid-associated proteins and major RNA polymerase σ initiation factors regulates growth phase-dependent gene transcription. We show that the highly conserved spatial ordering of relevant genes along the chromosomal replichores largely corresponds both to their temporal expression patterns during growth and to an inferred gradient of DNA superhelical density from the origin to the terminus. Genes implicated in similar functions are related mainly in trans across the chromosomal replichores, whereas DNA-binding transcriptional regulators interact predominantly with targets in cis along the replichores. We also demonstrate that macrodomains (the individual structural partitions of the chromosome) are regulated differently. We infer that spatial and temporal variation of DNA superhelicity during the growth cycle coordinates oxygen and nutrient availability with global chromosome structure, thus providing a mechanistic insight into how the organization of a complete bacterial chromosome encodes a spatiotemporal program integrating DNA replication and global gene expression.
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