In vivo DNase I sensitivity of the Streptomyces coelicolor chromosome correlates with gene expression: implications for bacterial chromosome structure

Abstract

For a bacterium, Streptomyces coelicolor A3(2) contains a relatively large genome (8.7 Mb) with a complex and adaptive pattern of gene regulation. We discovered a correlation between the physical structure of the S.coelicolor genome and the transcriptional activity of the genes therein. Twelve genes were surveyed throughout 72 h of growth for both in vivo sensitivity to DNase I digestion and levels of transcription. DNase I-sensitivity correlated positively with transcript levels, implying that it was predictive of gene expression, and indicating increased accessibility of transcribed DNA. The genome was fractionated based on the sensitivity to DNase I digestion, with the low molecular weight (frequently cut) fraction highly enriched for actively transcribed sequences when compared to the infrequently cut fraction, which was representative of the entire genome. This approach will allow comparison of nucleoid proteins, and any modifications thereof, associated with transcriptionally active and inactive regions of the bacterial genome.

Genes essential for morphological development and antibiotic production in Streptomyces coelicolor are targets of BldD during vegetative growth

“…Strikingly, when the entire genome was scanned, hundreds of BldD boxes were found within coding regions, although these intragenic sites were not bound by BldD in vivo , as determined by our ChIP‐chip experiment. Topological constraints of the DNA, or the presence of nucleoid proteins (McArthur and Bibb, 2006), might prevent BldD from interacting with predicted binding sites present within ORFs.…”

Molecular Regulation of Antibiotic Biosynthesis in Streptomyces

“…McArthur and Bibb developed an in vivo DNase I sensitivity method to monitor the correlation between the physical nucleoid and the transcriptional profile of Streptomyces. This approach provides an opportunity to characterize and compare the NAPs associated with the active and repressive portions of the nucleoid (289). If coupled with the decoy oligonucleotide technique developed by the same group (290), this approach can be used to identify histone-like proteins associated with antibiotic regulatory genes and to examine the role of these proteins in antibiotic production.…”

From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants

“…, 2009; Cichewicz, 2010). Intriguingly, histone‐like proteins that modulate the transcription of contiguous sets of genes, including those for secondary metabolic pathways, have recently been discovered in the actinomycete Streptomyces coelicolor (McArthur and Bibb, 2006, 2007). Evidence is emerging from the thalianol and avenacin clusters, both of which are developmentally regulated, to implicate chromatin remodelling in the regulation of plant secondary metabolic clusters.…”