Genome scale patterns of supercoiling in a bacterial chromosome

Abstract

DNA in bacterial cells primarily exists in a negatively supercoiled state. The extent of supercoiling differs between regions of the chromosome, changes in response to external conditions and regulates gene expression. Here we report the use of trimethylpsoralen intercalation to map the extent of supercoiling across the Escherichia coli chromosome during exponential and stationary growth phases. We find that stationary phase E. coli cells display a gradient of negative supercoiling, with the terminus being more negatively supercoiled than the origin of replication, and that such a gradient is absent in exponentially growing cells. This stationary phase pattern is correlated with the binding of the nucleoid-associated protein HU, and we show that it is lost in an HU deletion strain. We suggest that HU establishes higher supercoiling near the terminus of the chromosome during stationary phase, whereas during exponential growth DNA gyrase and/or transcription equalizes supercoiling across the chromosome.

Cooperative DnaA Binding to the Negatively Supercoiled datA Locus Stimulates DnaA-ATP Hydrolysis

“…DNA supercoiling is involved in regulation of multiple cellular processes, including DNA replication, transcription, recombination, and nucleoid compaction (19 -21). The supercoiling state of chromosomal DNA is altered dynamically according to the growth phase and extracellular stresses such as osmotic shock, heat, pH, and antibiotics to sustain cell growth (22)(23)(24)(25). For example, in the osmotic transcriptional response in E. coli, DNA supercoiling regulates the association of RNA polymerase on DNA and expression of osmotic-response genes (23,26 …”

“…The datA locus (991 bp) includes a 262-bp region containing two known DnaA-box sequences (DnaA boxes 2 and 3) and an IBS, which is essential for repression of untimely initiation ( Fig. 1A) (25)(26)(27)(28). DNA-footprinting experiments suggest the presence of two further sites within the 262-bp datA region that bind DnaA (herein described as DnaA boxes 6 and 7) ( Fig.…”

Requirement or exclusion of inverted repeat sequences with cruciform-forming potential in Escherichia coli revealed by genome-wide analyses

“…The negative supercoiling of DNA can induce the transition of some of IRs into cruciforms (Lilley 1980; Lilley and Markham 1983; Courey and Wang 1988; Paleček 1991; Van Holde and Zlatanova 1994; Shlyakhtenko et al 1998; Krasilnikov et al 1999; Oussatcheva et al 2004; Kouzine and Levens 2007). In vivo, the dynamic processes of DNA replication and transcription, which generate local underwinding and overwinding of DNA molecules, are the major causes for the generation of negative supercoils (Wu et al 1988; Schvartzman and Stasiak 2004; Kouzine et al 2013; Lal et al 2016). In cruciforms, the minimum length of the repeat unit sequence is generally 6–7 bp, but sometimes it is as short as 5 bp (Sheflin and Kowalski 1985; Iacono-Connors and Kowalski 1986; Müller and Wilson 1987; McMurray et al 1991; Dai et al 1997; Dai and Rothman-Denes 1998; Jagelská et al 2010; Nuñez et al 2015), and the typical number of nucleotides in a loop ranges from 3 to 6 (Hilbers et al 1985; Furlong and Lilley 1986; Gough et al 1986; Nag and Petes 1991; Sinden 1994; Potaman and Sinden 2005).…”

Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in E. coli

“…In this model, GalR protein indirectly regulates gene transcription as an architectural protein. We are currently studying the regional superhelicities in the entire chromosome in the presence and absence of GalR as well as the implication of genes affected by GalR, but independent of D-galactose metabolism (Lal et al, 2016). …”