TABLE 1.

Functional gene groups

Functional groupa	No. of genes	wt N2:wt O2b		Δfnr N2:Δfnr O2b		Δfnr N2:wt N2b
		Up	Down	Up	Down	Up	Down
Energy metabolism, carbon	61c	29	21	18	12	13	15
Central intermediary metabolism	12	3	5	3	1	7	2
Fatty acid and phosphatidic acid biosynthesis	2		1	1	1
Global regulatory functions	3		1	1		1
Macromolecule synthesis; modification: polysaccharides (cytoplasmic)	1					1
Ribosomal proteins: synthesis, modification	1					1
Purine ribonucleotide biosynthesis	1		1		1
Protein, peptide secretion	2	2
Cell division	1					1
Amino acid biosynthesis	3		1	1		1
Biosynthesis of cofactors; carriers: thiamine	1					1
2′-Deoxyribonucleotide metabolism	3	1				2
Degradation of proteins, peptides, glyco	1	1					1
Degradation of small molecules, carbon compounds	4	2				1	1
Detoxification	3		2		1	1
Drug and/or analog sensitivity	2			2		2
Outer membrane constituents	3	1		2		1	1
Osmotic adaptation	4		1	1		4
Chemotaxis and mobility	10				4		10
Surface structures	37			5	16	2	32
Transport of small molecules	22	7	9	2	7	4	6
Unknown	119	32	27	39	12	47	24
Total	297	78	69	75	55	90	92

^aFunctional group assignments are those described by Serres et al. (77). wt, wild type.

^bThe change (n-fold) between two experimental conditions was calculated by taking the ratio of the signal intensity (difference of the log₂ value) between two experimental conditions. Genes that showed at least a threefold increase in mRNA abundance relative to the control and had an average log₂ signal intensity greater than 8 were considered upregulated. Conversely, genes whose transcript abundance decreased more than threefold and had an average log₂ signal intensity greater than 8 in the control were considered downregulated.

^cThe same genes could appear in more than one comparison using this classification system.