Oscillations in supercoiling drive circadian gene expression in cyanobacteria

Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22564-8. doi: 10.1073/pnas.0912673106. Epub 2009 Dec 14.


The cyanobacterium Synechococcus elongatus PCC 7942 exhibits oscillations in mRNA transcript abundance with 24-h periodicity under continuous light conditions. The mechanism underlying these oscillations remains elusive--neither cis nor trans-factors controlling circadian gene expression phase have been identified. Here, we show that the topological status of the chromosome is highly correlated with circadian gene expression state. We also demonstrate that DNA sequence characteristics of genes that appear monotonically activated and monotonically repressed by chromosomal relaxation during the circadian cycle are similar to those of supercoiling-responsive genes in Escherichia coli. Furthermore, perturbation of superhelical status within the physiological range elicits global changes in gene expression similar to those that occur during the normal circadian cycle.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Chromosomes, Bacterial / genetics
  • Chromosomes, Bacterial / metabolism
  • Circadian Rhythm / genetics*
  • DNA Primers / genetics
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism
  • DNA, Superhelical / genetics
  • DNA, Superhelical / metabolism
  • Gene Expression Regulation, Bacterial
  • Genes, Bacterial*
  • Genome-Wide Association Study
  • Oligonucleotide Array Sequence Analysis
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Synechococcus / genetics*
  • Synechococcus / metabolism*
  • Systems Biology


  • DNA Primers
  • DNA, Bacterial
  • DNA, Superhelical
  • RNA, Bacterial
  • RNA, Messenger

Associated data

  • GEO/GSE18902