. 2006 Oct;72(10):6439–6451. doi: 10.1128/AEM.00398-06

TABLE 1.

Genes involved in specific processes and differentially expressed in wild-type (TT01) and luxS-deficient (PL2102) P. luminescens strains

Process	plu no.	Gene	Wild-type/luxS expression ratio at:		Function
Process	plu no.	Gene	Mid-exponential phase	End of exponential phase	Function
AI-2- and polyamine-related synthesis	plu0394^a	argD		4.70	Acetylornithine delta-aminotransferase
AI-2- and polyamine-related synthesis	plu0842^a	speD	0.41	S-Adenosylmethionine decarboxylase
	plu0843^a	speE		0.21	Spermidine synthase
	plu1307^a	gltI		2.18	Glutamate/aspartate ABC transport system permease
	plu2942^a			6.03	58% similarity with DNA-methyltransferase MunI, AdoMet dependent
	plu3141^a	lsrK		2.24	AI-2 kinase
	plu3146^a	lsrB		8.17	AI-2 binding protein of ABC transport system
	plu3147^a	lsrF		2.58	AI-2-processing aldolase
	plu3148^a	lsrG		3.20	AI-2-processing protein
	plu4397^a	metA		11.50	Homoserine O-succinyltransferase
	plu4420^a	metE		24.13	5-Methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
	plu4566^a			2.48	N-Dimethylarginine dimethylaminohydrolase family protein
	plu4567^a			2.52	Argininosuccinate synthase domain (arginine biosynthesis)
	plu4568^a			2.14	Putative cystathionine beta-synthase
	plu4743^a	argB		2.81	Cetylglutamate kinase (arginine biosynthesis)
	plu4756^a	metB		13.06	Cystathionine gamma-synthase
Oxidative stress	plu0842^a	speD		0.41	S-Adenosylmethionine decarboxylase
resistance	plu0843^a	speE		0.21	Spermidine synthase
	plu2027^a	uvrC		7.69	Excinuclease ABC subunit C
	plu2182	idgB	4.85		Indigoidine synthesis protein
	plu2496^a	adhE		2.74	Aldehyde-alcohol dehydrogenase
	plu2557^a	msrB		10.91	Peptide methionine sulfoxide reductase B
	plu3281^a	iscA		3.89	Iron binding protein IscA (iron-sulfur cluster)
	plu3282	iscU		2.02	Involved in formation of [Fe-S] clusters
	plu3343^a	rseC		3.20	Sigma-E factor regulatory protein
	plu4728^a	bfr	0.34		Bacterioferritin (cytochrome B-1, cytochrome B-557)
Motility and biofilm related
Flagellum regulon	plu1848^a	flhC		0.39	Flagellum biosynthesis transcription activator
	plu1912^a	flgN		0.36	Flagellum synthesis protein
	plu1945	fliI		0.22	Flagellum-specific ATP synthase
	plu4688	hdfR		0.49	H-NS-dependent flhDC regulator
Pili and fimbriae	plu0417			0.05	Putative fimbrial minor pilin subunit precursor
	plu0769^a	mrfA	2.13	3.59	Major fimbrial subunit polypeptide
	plu0782			0.36	Putative fimbrial chaperone protein
	plu0783			0.09	48% similarity with chaperone protein FimC precursor (E. coli O6)
	plu1053	pilP		0.04	Pilus assembly protein
	plu1056	pilS		0.21	Type IV prepilin
	plu1057	pilU		0.27	Prepilin peptidase
	plu1058	pilV		0.20	Type V prepilin
	plu1734			0.50	Type V prepilin-like
Other	plu1855^a	cheR	0.36		Chemotaxis protein methyltransferase
	plu4793^a	cpxP	0.47		Periplasmic protein precursor
	plu4795^a	cpxA		5.52	Sensory kinase in two-component regulatory system with CpxR
Virulence related	plu0635^a			0.15	Hemolysin secretion protein D (HlyD) family secretion protein
	plu0769^a	mrfA	2.13	3.59	Major fimbrial subunit polypeptide
	plu0884^a		0.32	2.70	Putative killer protein of pyocin S3
	plu0887^a			2.81	70% similarity with C-terminal region of klebicin B pyocin S2 and the killer protein of pyocin S1
	plu0888^a			2.52	50% similarity with colicin immunity protein operon
	plu0962^a	tcdA1		2.39	Insecticidal toxin complex protein TcdA1 (toxin A)
	plu1115			0.40	Syringomycin synthetase involved in antibiotic biosynthesis
	plu1356			0.22	64% similarity with hemolysin/hemagglutinin-like protein HecA precursor (Erwinia chrysanthemi)
	plu1665			2.73	Orf15 (Photorhabdus W14), C terminus similar to phage tail sheath protein
	plu1666			2.54	Orf14 (Photorhabdus W14), C terminus similar to Phage tail sheath protein FI
	plu1706^a		0.35		77% similarity with Orf15 (Photorhabdus W14), C terminus similar to phage tail sheath protein
	plu1878			0.24	Antibiotic synthetase
	plu1893		0.47		Colicin immunity protein
	plu1894		0.40		S-type pyocin
	plu2279	ccdB	0.33		Cytotoxic protein CcdB
	plu2393		4.32		Phage baseplate assembly protein W
	plu2753			0.23	84% similarity with hypothetical phage protein (Yersinia pestis)
	plu2875			0.21	60% similarity with hypothetical protein (bacteriophage Aaφ23)
	plu2902			0.30	Bacteriophage protein
	plu2905^a			2.84	Bacteriophage lambda endopeptidase
	plu2959		0.40		Putative tail fiber protein
	plu3026^a			10.84	59% similarity with putative bacteriophage protein STY2015 (S. enterica serovar Typhimurium)
	plu3028^a			11.28	68% similarity with putative bacteriophage protein STY2017 (S. enterica serovar Typhimurium)
	plu3029			0.43	73% similarity with putative bacteriophage protein STY2019 (S. enterica serovar Typhimurium)
	plu3030^a			7.62	61% similarity with putative bacteriophage protein STY2023 (S. enterica serovar Typhimurium)
	plu3031^a			11.28	57% similarity with putative bacteriophage protein STY2024 (S. enterica serovar Typhimurium)
	plu3035^a			16.28	78% similarity with putative bacteriophage protein STY2028 (S. enterica serovar Typhimurium)
	plu3036^a			14.03	69% similarity with putative bacteriophage protein STY2029 (S. enterica serovar Typhimurium)
	plu3037^a			12.58	69% similarity with putative bacteriophage protein STY2030 (S. enterica serovar Typhimurium)
	plu3123^a		0.48		Syringopeptin family antibiotic synthetase
	plu3126	rtxD		0.34	Toxin ABC transporter
	plu3127	rtxB		0.21	Toxin ABC transporter
	plu3128	mcf2		0.43	Toxin protein (Mcf-like protein)
	plu3238			0.04	Toxin motif IcmF in C-terminal region
	plu3385			0.34	52% similarity with hypothetical protein ORF45 (Burkholderia cepacia phage Bcep781)
	plu3428^a			5.06	Phage protein U
	plu3429^a			8.43	54% similarity with protein gp44 (Burkholderia cenocepacia phage BcepMu)
	plu3460^a			3.14	Mu-like prophage protein gp16
	plu3477			11.40	66% similarity with protein encoded by cryptic prophage CP-933P
	plu3780	sctE		0.15	Type III secretion component protein
	plu3781^a	sctF		7.71	Type III secretion component protein
	plu4167	tccC1		0.22	Insecticidal toxin complex protein TccC1
	plu4780		0.38		75% similarity with gpFI (bacteriophage Wφ)
	plu4781		0.49		Phage-related protein

The expression level was partially or completely restored to the wild-type level after the addition of AI-2 to the growth medium (see the text).