TABLE 4.

Examples of transcriptional changes of genes of known function in Δfur mutant (JW707) and wild-type D. vulgaris Hildenborough

Category/locus tag	Gene	Annotated function	SSDRa (mean ± SD) (n = 6)		Expression ratio (JW707/WT)
			JW707	WT
Genes in the predicted Fur regulonb
DVU0303	genZ	GenZ, hypothetical protein	2.16 ± 0.285	1.78 ± 0.172	2.11
DVU0304	genY	GenY, hypothetical protein	2.47 ± 0.277	2.15 ± 0.122	2.27
DVU0763	gdp	GGDEF domain protein	2.28 ± 0.321	1.96 ± 0.231	4.08
DVU0942	fur	Fur, transcriptional regulator	0.25 ± 0.036	2.16 ± 0.116	NDc
DVU2571	feoB	Ferrous iron transport protein B	1.97 ± 0.166	1.95 ± 0.142	1.96
DVU2572	feoA	Ferrous iron transport protein A	1.72 ± 0.321	1.83 ± 0.211	1.76
DVU2574	feoA	Ferrous ion transport protein	2.17 ± 0.277	1.93 ± 0.102	2.67
DVU2680	fld	Flavodoxin	1.88 ± 0.130	2.06 ± 0.133	1.50
Genes in the predicted PerR regulonb
DVU2247	ahpC	Antioxidant, AhpC/Tsa family	2.02 ± 0.220	2.03 ± 0.186	2.12
DVU2318	rbr	Rubrerythrin, putative	2.47 ± 0.277	1.76 ± 0.122	2.94
DVU3095	perR	PerR, transcriptional regulator	1.88 ± 0.213	1.90 ± 0.133	1.61
Other iron-related genes
DVU0646	cobI	Precorrin-2 C20-methyltransferase	1.28 ± 0.096	2.35 ± 0.182	0.30
DVU0647	COGfepB	Iron compound ABC transporter, iron-binding protein	0.93 ± 0.071	2.11 ± 0.171	0.14
DVU0648	fepC	Iron compound ABC transporter, ATP-binding protein	1.17 ± 0.277	1.84 ± 0.132	0.25
DVU0649	COGfepD	Iron compound ABC transporter, permease protein	1.20 ± 0.076	2.26 ± 0.119	0.28
DVU1397	bfr	Bacterioferritin	2.27 ± 0.217	2.16 ± 0.212	1.97
DVU1568	ftn	Ferritin	1.89 ± 0.173	2.33 ± 0.222	1.89

^aThe SSDR was calculated from Cy5-labeled cDNA signal, while Cy3-labeled gDNA was used for both JW707 and the wild type (WT).

^bPredicted by Rodionov et al. (25).

^cND, not determined due to lack of a Cy5 signal of the Δfur mutant.