DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle

Abstract

The chromosomal DNA polymer constituting the cellular genetic material is primarily a device for coding information. Whilst the gene sequences comprise the digital (discontinuous) linear code, physiological alterations of the DNA superhelical density generate in addition analog (continuous) three-dimensional information essential for regulation of both chromosome compaction and gene expression. Insight into the relationship between the DNA analog information and the digital linear code is of fundamental importance for understanding genetic regulation. Our previous study in the model organism Escherichia coli suggested that the chromosomal gene order and a spatiotemporal gradient of DNA superhelicity associated with DNA replication determine the growth phase-dependent gene transcription. In this study we reveal a general gradient of DNA thermodynamic stability correlated with the polarity of chromosomal replication and manifest in the spatiotemporal pattern of gene transcription during the bacterial growth cycle. Furthermore, by integrating the physical and dynamic features of the transcribed sequences with their functional content we identify spatiotemporal domains of gene expression encompassing different functions. We thus provide both an insight into the organisational principle of the bacterial growth program and a novel holistic methodology for exploring chromosomal dynamics.

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

“…Nevertheless, in bacteria, in addition to transcription-dependent torsional coupling, the maintenance of negative superhelical density by DNA gyrase is also crucial for the regulation of gene expression. Notably, the colocalization of gyrase binding sites with highly active and highly supercoil-dependent rrn genes (Sobetzko et al 2012(Sobetzko et al , 2013) implies a more nuanced complexity of regulation.…”

Interplay of digital and analog control in time-resolved gene expression profiles

“…Resulting expression curves were verified by fluorescence measurements of yfp-coupled promoters exhibiting different temporal patterns. The wild type data was first published in [31]. The fis and hns mutant strain data is new to this work.…”

“…Before application of the newly defined methods, we present an impression of the timeresolved RNA-seq data measured in the wild type (first published in [31]) and the two mutants fis and hns. The relevant experiments and data transformations are described in Sections "Cell growth conditions and mRNA isolation" and "Gene expression analysis".…”

“…2 Interpolated and normalized gene expression levels. a The levels published in [31] are shown here normalized between zero and unity. There are seven examples of gene levels in the wild type: fis, which is prominent in the early to mid exponential growth phase; hns, strongly expressed in the late exponential growth phase;the σ 70 -factor encoding gene rpoD which is more active during exponential growth; the σ S -factor encoding gene rpoS, mostly active during the transition from late exponential to stationary growth phase; dps, which is associated with the stationary phase; and the two gyrase-encoding genes gyrA and gyrB.…”

“…The results of a wide range of our own investigations over the last years have their foundations in statistical physics and information theory [2,4,[25][26][27][28][29][30][31]. They have cemented the notion of a tight interplay of the regulatory network implemented via TFs and their binding sites (digital control); and the regulation implemented via alterations of chromosomal configuration and DNA compaction (analog control) in bacterial gene regulation (depicted in Fig.…”