TABLE 1.

Selected results from swarm versus swim RNA-Seq comparisons^a

Locus tag	PAO1	Name	Product name	Padj	FCb
Transcriptional regulators, two-component systems and sigma factors
PA14_00600	PA0048		Transcriptional regulator	9.1E−06	1.7
PA14_00680	PA0056		LysR family transcriptional regulator	2.0E−03	1.5
PA14_02250	PA0178		Two-component sensor	5.2E−09	1.6
PA14_02260	PA0179		Two-component response regulator	4.4E−07	1.5
PA14_02390	PA0191		Transcriptional regulator	3.4E−08	−2.0
PA14_02870	PA0233		Transcriptional regulator	1.9E−08	1.5
PA14_03070	PA0248		Transcriptional regulator	9.0E−06	1.6
PA14_03580	PA0275		Transcriptional regulator	9.8E−07	1.5
PA14_04820	PA0367	laoR	TetR family transcriptional regulator	4.4E−14	1.6
PA14_06170	PA0471	fiuR	Transmembrane sensor	1.0E−04	1.7
PA14_06180	PA0472	fiuI	RNA polymerase sigma factor	3.0E−05	1.5
PA14_06690	PA0513	nirG	Transcriptional regulator	1.8E−13	−3.2
PA14_06710	PA0515		Transcriptional regulator	5.4E−13	−3.4
PA14_06770	PA0520	nirQ	Regulatory protein	4.6E−21	−2.9
PA14_06970	PA0535		Cro/CI family transcriptional regulator	2.5E−09	−1.6
PA14_07110	PA0547		ArsR family transcriptional regulator	8.7E−27	1.7
PA14_09260	PA4227	pchR	Transcriptional regulator	5.6E−28	3.8
PA14_09680	PA4197	bfiS	Two-component sensor	5.4E−09	−1.7
PA14_09790	PA4182		Transcriptional regulator	1.3E−13	−1.5
PA14_10530	PA4132		GntR family transcriptional regulator	2.0E−28	−1.5
PA14_10660	PA4120		Transcriptional regulator	7.9E−05	1.9
PA14_10940	PA4094		AraC family transcriptional regulator	2.0E−06	1.6
PA14_11120	PA4080		Response regulator	6.9E−08	1.5
PA14_12140	PA3995		Transcriptional regulator	1.3E−09	1.7
PA14_13000	PA3932		Transcriptional regulator	1.2E−14	−2.7
PA14_13150	PA3921		Transcriptional regulator	1.6E−14	1.5
PA14_15240	PA3776		LysR family transcriptional regulator	1.3E−03	−1.6
PA14_15290	PA3771		Transcriptional regulator	7.9E−06	1.9
PA14_15830	PA3757	nagR	GntR family transcriptional regulator	2.9E−05	−1.5
PA14_16790	PA3678	mexL	TetR family transcriptional regulator	6.8E−15	1.5
PA14_17380	PA3630	gfnR	Glutathione-dependent formaldehyde neutralization regulator	7.1E−11	1.8
PA14_17480	PA3622	rpoS	RNA polymerase sigma factor	1.9E−11	1.6
PA14_17540	PA3616		Recombination regulator RecX	6.3E−10	−1.6
PA14_19380	PA3458		Transcriptional regulator	3.8E−08	1.8
PA14_19990	PA3410	hasI	RNA polymerase ECF-subfamily sigma-70 factor	3.6E−06	−2.0
PA14_20230	PA3391	nosR	Regulatory protein	2.1E−37	−17.2
PA14_20780	PA3346	hsbR	Two-component response regulator	2.6E−20	1.6
PA14_23190	PA3174	hutR	Transcriptional regulator	1.1E−12	−2.2
PA14_23590	PA3133	sawR	Transcriptional regulator	5.2E−11	−2.1
PA14_24710	PA3045	rocA2	Two-component response regulator	9.1E−11	−2.5
PA14_24720	PA3044	rocsS2	Two-component sensor	5.2E−14	−2.1
PA14_25800	PA2957		TetR family transcriptional regulator	3.5E−13	−1.5
PA14_26330	PA2917		AraC family transcriptional regulator	4.4E−18	−2.3
PA14_26860	PA2879		LysR family transcriptional regulator	3.2E−19	2.0
PA14_30580	PA2591	vqsR	LuxR family transcriptional regulator	2.5E−21	1.6
PA14_30840	PA2571		Signal transduction histidine kinase	7.2E−09	1.5
PA14_32060	PA2519	xylS	Transcriptional regulator	3.6E−08	1.8
PA14_32460	PA2488		Transcriptional regulator	7.7E−04	1.5
PA14_32710	PA2468	foxI	ECF subfamily RNA polymerase sigma-70 factor	5.8E−05	1.8
PA14_32720	PA2467	foxR	Transmembrane sensor	1.7E−04	1.5
PA14_33260	PA2426	pvdS	Extracytoplasmic-function sigma-70 factor	9.7E−07	2.0
PA14_33440	PA2417		LysR family transcriptional regulator	3.5E−09	1.6
PA14_33800	PA2387	fpvI	RNA polymerase sigma factor	1.8E−33	2.2
PA14_33840	PA2383		Transcriptional regulator	4.3E−17	2.9
PA14_34440	PA2337	mtlR	Transcriptional regulator	1.7E−04	1.5
PA14_34660	PA2320	gntR	Transcriptional regulator	1.3E−19	1.6
PA14_34730	PA2312		XRE family transcriptional regulator	3.5E−15	−3.0
PA14_34820	PA2304	ambC	Regulatory protein	2.7E−20	3.5
PA14_34830	PA2303	ambD	Regulatory protein	1.2E−30	3.6
PA14_34880	PA2299		GntR family transcriptional regulator	7.2E−14	2.0
PA14_35250	PA2267		LysR family transcriptional regulator	1.5E−06	1.6
PA14_35370	PA2259	ptxS	Transcriptional regulator	1.3E−08	−2.1
PA14_35380	PA2258	ptxR	Transcriptional regulator	1.7E−13	2.4
PA14_36300	PA2196		TetR family transcriptional regulator	5.0E−10	1.6
PA14_36420	PA2177		Sensor/response regulator hybrid	3.7E−18	2.3
PA14_36990	PA2133		Cyclic-guanylate-specific phosphodiesterase	4.8E−03	−1.9
PA14_37140	PA2121		LysR family transcriptional regulator	4.0E−03	1.6
PA14_37420	PA2094		Transmembrane sensor protein	7.9E−13	3.7
PA14_37430	PA2093		RNA polymerase sigma factor	2.4E−07	2.5
PA14_37580	PA2082	kynR	Leucine-responsive regulatory protein	1.6E−04	1.5
PA14_37980	PA2051		Fe2+ dicitrate sensor, membrane protein	5.8E−08	−3.3
PA14_37990	PA2050		RNA polymerase sigma factor	1.5E−13	−4.5
PA14_38250	PA2032		Transcriptional regulator	8.7E−18	1.6
PA14_39800	PA1912	femI	ECF subfamily RNA polymerase sigma-70 factor	2.6E−03	−1.6
PA14_39980	PA1898	qscR	Transcriptional regulator	2.7E−07	1.7
PA14_42390	PA1713	exsA	Transcriptional regulator	1.3E−24	2.7
PA14_45250	PA1484		Transcriptional regulator	5.6E−05	1.5
PA14_45950	PA1431	rsaL	Regulatory protein	2.1E−74	3.0
PA14_46290	PA1403		TetR family transcriptional regulator	4.2E−07	2.0
PA14_46810	PA1351		RNA polymerase ECF-subfamily sigma-70 factor	1.7E−10	1.9
PA14_47390	PA1301		Transmembrane sensor	2.4E−03	1.6
PA14_48160	PA1243		Sensor/response regulator hybrid	1.4E−40	3.2
PA14_48830	PA1196	ddaR	Transcriptional regulator	2.7E−07	1.6
PA14_49170	PA1180	phoQ	Two-component sensor	4.7E−16	−2.0
PA14_49180	PA1179	phoP	Two-component response regulator	5.5E−14	−1.8
PA14_49790	PA1128		Transcriptional regulator	1.9E−05	1.7
PA14_53410	PA0839		Transcriptional regulator	2.7E−04	−1.5
PA14_53720	PA0816		Transcriptional regulator	2.1E−10	1.8
PA14_55160	PA0707	toxR	Transcriptional regulator	2.4E−17	5.5
PA14_55550	PA0675	vreI	ECF subfamily RNA polymerase sigma-70 factor	8.4E−10	−2.6
PA14_55780	PA4293	pprA	Two-component sensor	8.6E−18	2.5
PA14_57140	PA4396		Two-component response regulator	1.5E−17	1.6
PA14_58380	PA4499	psdR	Transcriptional regulator	7.2E−10	−1.6
PA14_58510	PA4508		AsnC family transcriptional regulator	7.7E−06	−1.6
PA14_61620	PA4659		MerR family transcriptional regulator	2.0E−11	−1.9
PA14_63280	PA4787		Transcriptional regulator	1.6E−13	1.6
PA14_64050	PA4843	gcbA	Two-component response regulator	2.1E−48	−1.9
PA14_64500	PA4878	brlR	Transcriptional regulator	1.6E−13	−1.8
PA14_64690	PA4895		Transmembrane sensor	3.3E−06	−1.8
PA14_64700	PA4896		RNA polymerase sigma factor	1.3E−05	−1.9
PA14_66850	PA5059		TetR family transcriptional regulator	1.1E−09	1.7
PA14_69470	PA5261	algR	Alginate biosynthesis regulatory protein	2.3E−12	1.6
PA14_71170	PA5389	cdhR	AraC family transcriptional regulator	1.1E−03	1.6
PA14_71750	PA5437		LysR family transcriptional regulator	2.5E−79	−3.3
PA14_72380	PA5483	algB	Two-component response regulator	2.3E−11	1.9
PA14_72390	PA5484	kinB	Two-component sensor	1.4E−16	1.9
Multidrug efflux and β-lactamases
PA14_01940	PA0156	triA	RND efflux membrane fusion protein	6.6E−12	1.6
PA14_09500	PA4208	opmD	Outer membrane protein	1.3E−22	1.8
PA14_09520	PA4207	mexI	RND efflux transporter	2.0E−23	1.6
PA14_18760	PA3523	mexP	RND efflux membrane fusion protein	3.1E−10	−4.0
PA14_18780	PA3522	mexQ	RND efflux transporter	1.5E−31	−3.4
PA14_18790	PA3521	opmE	Outer membrane efflux protein	1.2E−12	−3.3
PA14_32390	PA2494	mexF	RND multidrug efflux transporter	3.6E−14	−2.0
PA14_32400	PA2493	mexE	RND multidrug efflux membrane fusion protein	4.2E−11	−1.9
PA14_38395	PA2019	mexX	Periplasmic multidrug efflux lipoprotein	3.4E−07	−1.8
PA14_38410	PA2018	mexY	Multidrug efflux protein	2.1E−06	−1.6
PA14_41280	PA1797		β-Lactamase	2.8E−11	2.0
PA14_44520	PA1541		Drug efflux transporter	1.5E−10	−5.6
PA14_44530	PA1540		Multidrug efflux system protein MdtI	6.7E−05	−2.4
PA14_45910	PA1435		RND efflux membrane fusion protein	1.1E−02	−1.6
PA14_48240	PA1238		Outer membrane component of multidrug efflux pump	4.3E−02	1.7
PA14_54700	PA0740	sdsA1	β-Lactamase	1.5E−03	−1.5

^aThese revealed 104 dysregulated transcriptional regulators and dysregulated efflux and β-lactamase genes.

^bFC, fold change.