Table 1.

Genes that are differentially regulated in the Ng-ntrX mutant compared to the 1291 wild-type strain

Gene type and no.a	Product description (gene)	ntrX mutant/WT expression ratio by:
		Microarray (B statistic)b	Enzyme activityc
Downregulated
NGO1276	Nitrite reductase (aniA)	0.33 (6.91)	0.29
NGO1275	Nitric oxide reductase (norB)	0.37 (4.09)
NGO1769	Cytochrome c peroxidase (ccpR)	0.39 (4.19)
NGO1371	Cytochrome oxidase subunit (ccoP)	0.40 (5.23)	0.46
NGO1024	Hypothetical protein	0.40 (5.13)
NGO1064	CstA	0.45 (2.18)
NGO0718	Putative RpiR family transcriptional regulator	0.50 (4.77)
Upregulated
NGO0641	Putative type III restriction/modification methylase	2.64 (1.01)
NGO0640	RmsR	2.62 (3.70)
NGO1712	Hypothetical protein	2.15 (5.15)
NGO1889	Hypothetical protein	2.07 (3.67)

^aThe “NGO” gene identification numbers refer to the annotation of the Neisseria gonorrhoeae strain FA1090 genome in the Los Alamos database (http://www.stdgen.lanl.gov/stdgen/bacteria/ngon/index.html).

^bThe ratio presented is the mean of the ratio of expression of the mutant to that of the wild type (WT) from six replicate spots on three independent microarrays, incorporating a dye swap. Thus, the expression of each gene was measured six times. Only those genes with an expression value above 2-fold (upregulated) or below 0.5-fold (downregulated) and having a B statistic value above 0.0 were considered significant and included in this study. A threshold in the B statistic of 0.0 was adopted because genes with a B score of >0 have a >50% probability of being truly differentially expressed.

^cEnzyme assays were performed as detailed in Materials and Methods, and the results are detailed in Fig. S1 in the supplemental material.