TABLE 2.

Differentially expressed genes in the pilR and rpoN mutants

Gene IDa	Putative function	pilR/WT expression ratio		rpoN/WT expression ratio		σ54 promoter distance (bp)e	Evidence and/or function
		Microarrayb	QRT-PCRc	Microarray	QRT-PCR
gdn1074	FimA	0.23	0.00078 ± 0.00043	0.15	0.012 ± 0.0081	75	FimA D. nodosus
gdn1291	Outer membrane protein	0.29	NTd	0.39	NT	383	Signal sequence, outer membrane OprF of Pseudomonas stutzeri, 37% identity
gdn1292	Outer membrane RTX protein	0.58 (P < 0.15)	0.12 ± 0.06	0.39	0.07 ± 0.02		PSI-BLAST: RTX toxin, leukotoxins
gdn1328	Lipoprotein	0.58 (P < 0.007)	NT	0.64	NT	43	Lipoprotein signal sequence with 61% identity to NMA1549
gdn1329	Unknown	0.57 (P < 0.006)	0.12 ± 0.03	0.46	0.09 ± 0.04		Conserved hypothetical protein
gdn1330	Inner membrane protein	0.31	0.12 ± 0.05	0.44	0.11 ± 0.02		COG1585 membrane protein implicated in regulation of membrane protease activity
gdn1331	Inner membrane protease	0.39	0.16 ± 0.04	0.63	0.19 ± 0.11		COG0330 HflC membrane protease subunit

^aNumbers refer to the annotation at the time of this writing.

^bAll expression ratios presented are significant (P < 0.005) unless otherwise stated.

^cQRT-PCR ratios are significant (P < 0.02).

^dNT, not tested.

^eDistance of the potential σ⁵⁴ binding site from the ATG of the first gene in the operon.