Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 109, Issue 2, Pages E42-E50Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1108229109
Keywords
gene order conservation; transcriptional regulatory network; protein gradients
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Funding
- Ecole Normale Superieure de Cachan
- Deutsche Forschungsgemeinschaft
- l'Agence Nationale de la Recherche
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In Escherichia coli crosstalk between DNA supercoiling, nucleoid-associated proteins and major RNA polymerase sigma 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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