Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

Peter, Brian J; Arsuaga, Javier; Breier, Adam M; Khodursky, Arkady B; Brown, Patrick O; Cozzarelli, Nicholas R

doi:10.1186/gb-2004-5-11-r87

Table 1 Plasmid supercoiling measurements from relaxation experiments

From: Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

Genotype	Experimental treatment	Plasmid σ	Model ratio
gyrA ^R parC ^R	15 μg/ml Nor, 0 min	-0.057	1.0
gyrA ^R parC ^R	15 μg/ml Nor, 2 min	-0.057	1.0
gyrA ^R parC ^R	15 μg/ml Nor, 5 min	-0.057	1.0
gyrA ^R parC ^R	15 μg/ml Nor, 10 min	-0.057	1.0
gyrA ^R parC ^R	15 μg/ml Nor, 20 min	-0.060	1.0
gyrA ^R parC ^R	15 μg/ml Nor, 30 min	-0.060	0.9
gyrA ^R parC ^R	50 μg/ml Nor, 0 min	-0.057	1.0
gyrA ^R parC ^R	50 μg/ml Nor, 2 min	-0.057	1.0
gyrA ^R parC ^R	50 μg/ml Nor, 5 min	-0.057	1.0
gyrA ^R parC ^R	50 μg/ml Nor, 10 min	-0.058	1.0
gyrA ^R parC ^R	50 μg/ml Nor, 20 min	-0.059	1.0
gyrA ^R parC ^R	50 μg/ml Nor, 30 min	-0.061	0.9
gyrB ⁺	37°C	-0.059	1.0
gyrB ⁺	42°C, 2 min	-0.059	1.0
gyrB ⁺	42°C, 5 min	-0.059	1.0
gyrB ⁺	42°C, 10 min	-0.059	1.0
gyrB ⁺	42°C, 20 min	-0.061	1.0
gyrB ^TS	37°C	-0.044	1.0
gyrB ^TS	42°C, 2 min	-0.023	1.6
gyrB ^TS	42°C, 5 min	-0.016	1.8
gyrB ^TS	42°C, 10 min	ND	ND
gyrB ^TS	42°C, 20 min	0.000	2.5
gyrA ⁺ parC ^R	15 μg/ml Nor, 0 min	-0.057	1.0
gyrA ⁺ parC ^R	15 μg/ml Nor, 2 min	-0.025	1.7
gyrA ⁺ parC ^R	15 μg/ml Nor, 5 min	-0.009	2.2
gyrA ⁺ parC ^R	15 μg/ml Nor, 10 min	-0.006	2.3
gyrA ⁺ parC ^R	15 μg/ml Nor, 20 min	-0.002	2.4
gyrA ⁺ parC ^R	15 μg/ml Nor, 30 min	0.000	2.5
gyrA ⁺ parC ⁺	50 μg/ml Nor, 0 min	-0.057	1.0
gyrA ⁺ parC ⁺	50 μg/ml Nor, 2 min	-0.016	1.9
gyrA ⁺ parC ⁺	50 μg/ml Nor, 5 min	-0.002	2.4
gyrA ⁺ parC ⁺	50 μg/ml Nor, 10 min	0.000	2.5
gyrA ⁺ parC ⁺	50 μg/ml Nor, 20 min	0.007	2.8
gyrA ⁺ parC ⁺	50 μg/ml Nor, 30 min	0.016	3.2
gyrA ⁺ parC ⁺	15 μg/ml Nor, 0 min	-0.055	1.0
gyrA ⁺ parC ⁺	15 μg/ml Nor, 10 sec	-0.048	1.1
gyrA ⁺ parC ⁺	15 μg/ml Nor, 25 sec	-0.040	1.3
gyrA ⁺ parC ⁺	15 μg/ml Nor, 45 sec	-0.032	1.5
gyrA ⁺ parC ⁺	15 μg/ml Nor, 1 min	-0.027	1.6
gyrA ⁺ parC ⁺	15 μg/ml Nor, 1.5 min	-0.022	1.7
gyrA ⁺ parC ⁺	15 μg/ml Nor, 2 min	-0.017	1.9
gyrA ⁺ parC ⁺	15 μg/ml Nor, 3 min	-0.012	2.1
gyrA ⁺ parC ⁺	15 μg/ml Nor, 4 min	-0.008	2.2
gyrA ⁺ parC ⁺	15 μg/ml Nor, 5 min	-0.003	2.4
gyrA ⁺ parC ⁺	15 μg/ml Nor, 7 min	0.000	2.5
gyrA ⁺ parC ⁺	15 μg/ml Nor, 10 min	0.003	2.6
gyrA ⁺ parC ⁺	15 μg/ml Nor, 15 min	0.002	2.6
gyrA ⁺ parC ⁺	15 μg/ml Nor, 20 min	0.000	2.5
ΔacrA	0 μg/ml Novo, 0 min	-0.057	1.0
ΔacrA	20 μg/ml Novo, 5 min	-0.011	2.1
ΔacrA	50 μg/ml Novo, 5 min	0.005	2.7
ΔacrA	200 μg/ml Novo, 5 min	0.011	3.0

pBR322 plasmid DNA was isolated from cells and analyzed by electrophoresis. Experimental treatments in bold indicate samples taken immediately before addition of drug or temperature shift, which were used as a reference for the following time points. Model ratios represent values derived from plasmid σ by taking the ratio of σ in each time point and dividing by σ in the reference, and scaling that value such that a sigma of 0 corresponds to a model ratio of 2.5. Nor, norfloxacin; Novo, novobiocin; SSG, supercoiling-sensitive gene; TS, temperature-sensitive. ND, not determined.

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