TABLE 4.

Genes up regulated in PAKmucA22

ID no.a	Gene	Function	Fold change in mucA22 vs wild type	TSBb (fold)	LBb (fold)
PA0059	osmC	Adaptation, protection	3.75	1.23	−1.29
PA2386	pvdA	Adaptation, protection	3.89	−1.50	1.07
#PA2397	pvdE	Adaptation, protection, membrane proteins, transport of small molecules	3.92	−3.00	−1.99
PA2401		Adaptation, protection	3.06	−1.00	−5.74
PA4468	sodM	Adaptation, protection	5.60	−1.30	1.02
PA2018		Antibiotic resistance and susceptibility, membrane proteins, transport of small molecules	3.88	−1.50	1.65
PA2019		Antibiotic resistance and susceptibility, transport of small molecules	4.16	−1.50	−1.36
PA1985	pqqA	Biosynthesis of cofactors, prosthetic groups, and carriers	2.99	−1.10	−1.24
PA1988	pqqD	Biosynthesis of cofactors, prosthetic groups, and carriers	3.18	−1.50	−1.28
PA1989	pqqE	Biosynthesis of cofactors, prosthetic groups, and carriers	3.00	1.44	−1.34
#PA2414		Carbon compound catabolism	5.17	−3.00	−1.29
PA3158	wbpB	Cell wall, LPS, and capsule; putative enzymes	5.76	−1.20	−1.08
PA0102		Central intermediary metabolism	3.38	−2.40	−1.15
PA2393		Central intermediary metabolism	3.27	−1.70	−4.76
PA2717	cpo	Central intermediary metabolism	4.75	1.21	−1.72
PA4470	fumC1	Energy metabolism	5.81	1.05	−1.62
PA5491		Energy metabolism	2.97	−1.30	1.08
#PA0320		Hypothetical	3.86	−7.80	−1.43
PA0586		Hypothetical	5.10	1.61	1.96
PA0587		Hypothetical	4.57	1.11	1.64
PA0588		Hypothetical	4.57	1.12	1.64
PA0613		Hypothetical	3.60	1.14	−1.55
#PA0737		Hypothetical	10.80	1.70	−1.00
PA0807		Hypothetical	3.97	1.21	−1.52
PA0990		Hypothetical	3.45	2.31	−1.48
PA1245		Hypothetical; membrane proteins	5.12	−1.10	−1.20
PA1323		Hypothetical	4.21	1.94	2.25
#PA1471		Hypothetical	12.4	1.46	1.07
#PA1784		Hypothetical	6.71	1.33	−1.31
PA1852		Hypothetical	3.34	1.90	−1.03
PA2159		Hypothetical	3.56	1.44	−2.46
PA2161		Hypothetical	2.95	1.50	−4.92
#PA2167		Hypothetical	9.54	1.16	−1.06
PA2168		Hypothetical	3.20	−1.20	−2.80
#PA2172		Hypothetical	3.86	−1.90	−1.99
PA2176		Hypothetical	7.30	1.79	2.10
PA2403		Hypothetical; membrane proteins	4.96	−1.30	−1.52
PA2404		Hypothetical; membrane proteins	5.83	1.27	−1.69
#PA2405		Hypothetical	10.00	1.10	−5.91
PA2406		Hypothetical	5.79	−1.10	−1.22
PA2412		Hypothetical	4.56	−1.30	−2.72
PA2485		Hypothetical	5.16	−1.20	5.51
PA2486		Hypothetical	6.30	1.17	1.41
PA2562		Hypothetical	3.30	1.27	2.38
PA3274		Hypothetical	5.30	1.61	−2.16
PA4154		Hypothetical	3.63	1.49	1.08
#PA4469		Hypothetical	8.78	−1.30	−1.64
PA4471		Hypothetical	3.00	−1.00	−3.49
PA5182		Hypothetical; membrane proteins	4.81	1.29	2.11
PA5183		Hypothetical; membrane proteins	3.88	1.20	2.02
PA5212		Hypothetical	3.24	1.32	1.83
PA2409		Membrane proteins, transport of small molecules	4.21	−1.20	−1.46
PA4876	osmE	Membrane proteins, adaptation, protection	3.00	1.36	1.27
PA2407		Motility and attachment	4.73	−1.20	−1.61
PA2385		Putative enzymes	3.19	1.05	−2.36
PA2394		Putative enzymes	3.56	1.00	−1.75
PA2402		Putative enzymes	3.18	−1.70	−2.00
PA2413		Putative enzymes	5.97	1.46	−2.32
PA4785		Putative enzymes	4.51	1.70	−1.98
PA0724		Related to phage, transposon, or plasmid	3.48	1.83	−2.39
PA1300		Transcriptional regulators	3.66	−1.70	−1.13
PA2426	pvdS	Transcriptional regulators	4.39	−1.40	−1.38
PA2408		Transport of small molecules	4.09	2.08	−3.14
PA3049	rmf	Translation, posttranslational modification, degradation	6.81	2.03	1.38
PA3188		Transport of small molecules	3.08	4.04	15.76
PA5470		Translation, posttranslational modification, degradation	3.31	−1.50	1.15
#PA2398	fpvA	Transport of small molecules	6.65	−2.10	−1.51

^a#, up regulated in mucA mutant compared to PAK, but down regulated in PAK under type III-inducing conditions versus noninducing conditions, and vice versa. Not included are those known to be affected by the growth medium, such as those varied in TSB versus LB (44).

^bChange in gene expression in PAK grown under T3SS-inducing conditions versus PAK grown under non-T3SS-inducing conditions (44). Bacteria were grown in TSB or LB.