Table 2.

Genes down- and upregulated by ralp3 knockout in S. pyogenes M49 (strain 591)^a

ORF	Gene	Description	Log2 expression ratio
			Array 1	Array 2	Avg	SD	qRT-PCRb
Downregulated genes
spy49_0162	opuABC	l-Proline glycine betaine ABC transport system permease	−1.75	−1.69	−1.72	0.05	NT
spy49_0254c		Transposase	−1.65	−1.71	−1.68	0.04	NT
spy49_0343		Hypothetical protein	−2.09	−2.04	−2.07	0.03	NT
spy49_0344		Hypothetical protein	−2.00	−1.97	−1.99	0.02	NT
spy49_0347		Hypothetical protein	−2.36	−2.40	−2.38	0.03	NT
spy49_0672	fruR	Putative transcriptional repressor	−1.64	−1.64	−1.64	0.00	−1.61 ± 0.88
spy49_0673	fruK	Tagatose-6-phosphate kinase/1-phosphofructokinase	−1.65	−1.69	−1.67	0.03	−1.80 ± 0.98
spy49_0674	fruA	PTS system, fructose-specific IIABC component	−1.82	−1.87	−1.84	0.04	NT
spy49_0830	sclB	SclB protein	−2.60	−2.64	−2.62	0.02	NT
spy49_1024		Hypothetical protein	−1.68	−1.71	−1.69	0.02	NT
spy49_1321c		Hypothetical protein	−1.68	−1.72	−1.70	0.03	NT
spy49_1322c	lacD1	Tagatose 1,6-diphosphate aldolase	−2.08	−2.07	−2.07	0.01	NT
spy49_1323c	lacC1	Tagatose-6-phosphate kinase/1- phosphofructokinase	−2.10	−2.08	−2.09	0.01	NT
spy49_1324c		Tagatose-6-phosphate kinase/1- phosphofructokinase	−2.09	−2.08	−2.09	0.00	NT
spy49_1325c	lacB	Galactose-6-phosphate isomerase subunit LacB	−1.81	−1.80	−1.81	0.01	NT
spy49_1326c	lacA	Galactose-6-phosphate isomerase subunit LacA	−1.73	−1.76	−1.75	0.02	−1.97 ± 0.75
spy49_1577c	salK	SalK	−1.71	−1.67	−1.69	0.02	NT
spy49_1578c	salY	Putative ABC transporter	−2.57	−2.69	−2.63	0.08	NT
spy49_1579c	salX	Putative salivaricin A ABC transporter	−3.58	−3.95	−3.77	0.26	NT
spy49_1580c	salT	Putative salivaricin A modification enzyme	−3.52	−4.58	−4.05	0.75	−4.21 ± 1.08
spy49_1582c	salB	Putative salivaricin A modification enzyme, amino acid dehydration	−3.37	−4.57	−3.97	0.85	NT
spy49_1583c	salA	Lantibiotic salivaricin A precursor	−5.75	−5.71	−5.73	0.03	−6.01 ± 0.45
spy49_1584c	lacG	6-Phospho-β-galactosidase	−5.80	−5.88	−5.84	0.06	NT
spy49_1585c	lacE	PTS system, lactose-specific IIBC component (EIIBC-Lac)	−4.94	−4.98	−4.96	0.03	−5.45 ± 1.08
spy49_1586c	lacF	PTS system, lactose-specific IIA component (EIIA-Lac)	−4.59	−4.56	−4.57	0.02	NT
spy49_1587c	lacD2	Tagatose 1,6-diphosphate aldolase	−4.26	−4.42	−4.34	0.12	NT
spy49_1588c	lacC2	Tagatose-6-phosphate kinase	−3.50	−3.64	−3.57	0.10	NT
spy49_1589c	lacB2	Galactose-6-phosphate isomerase subunit LacB	−2.70	−2.66	−2.68	0.03	NT
spy49_1590c	lacA2	Galactose-6-phosphate isomerase subunit LacA	−2.62	−2.66	−2.64	0.03	−1.61 ± 2.08
spy49_1633c	sclA	Collagen-like surface protein	−3.35	−3.39	−3.37	0.03	NT
spy49_1668c		Cell surface/fibronectin-binding protein	−3.77	−3.89	−3.83	0.08	NT
spy49_1670c	ennX	EnnX protein	−2.86	−2.86	−2.86	0.00	NT
spy49_1671c	emm49	Antiphagocytic M protein	−4.45	−4.51	−4.48	0.04	−5.16 ± 0.65
spy49_1672c		Fc-gamma receptor	−2.79	−2.76	−2.77	0.02	NT
spy49_1673c	mga	M protein trans-acting positive regulator (Mga)	−1.58	−1.81	−1.70	0.17	−1.36 ± 0.16
spy49_1683c	sfbX49	Fibronectin-binding protein	−2.97	−3.06	−3.01	0.06	NT
spy49_1684c	sof	Serum opacity factor	−2.54	−3.03	−2.78	0.35	−2.71 ± 0.90
spy49_1686		Hypothetical protein	−1.73	−2.30	−2.02	0.40	NT
spy49_1687c	ropA	Proteinase maturation protein (RopA)	−3.18	−3.15	−3.16	0.02	NT
spy49_1688c		Hypothetical protein	−3.07	−3.08	−3.08	0.01	NT
spy49_1689c		Spi SpeB protease inhibitor	−3.00	−3.09	−3.04	0.06	NT
spy49_1690c	speB	Streptococcal pyrogenic exotoxin B (SpeB)	−2.79	−2.87	−2.83	0.06	NT
spy49_1719c	csp	Major cold-shock protein	−1.90	−1.80	−1.85	0.07	NT
Upregulated genes
spy49_0564c		Transposase	2.45	2.47	2.46	0.01	NT
spy49_0565c		Transposase	2.51	2.43	2.47	0.06	NT
spy49_0863	malP	Putative l-malate permease	2.03	2.06	2.05	0.02	1.13 ± 0.50
spy49_0864		NAD-dependent malic enzyme	2.33	2.25	2.29	0.06	NT
spy49_1114c		Putative 16S pseudouridylate synthetase	2.13	2.26	2.20	0.09	NT
spy49_1115c	nagB	Glucosamine-6-phosphate deaminase	2.80	2.97	2.88	0.12	NT
spy49_1239		Alpha-mannosidase	1.53	1.63	1.58	0.07	NT
spy49_1332c	copA	Putative copper-transporting ATPase	2.18	2.18	2.18	0.00	NT
spy49_1334c	copY	Negative transcriptional regulator, CopY	1.86	1.87	1.87	0.01	2.41 ± 0.12
spy49_1374c	dnaK	Molecular chaperone DnaK	1.61	1.50	1.56	0.08	NT
spy49_1375c	grpE	Heat shock protein GrpE	2.21	2.25	2.23	0.03	NT
spy49_1376c	hrcA	Heat-inducible transcription repressor	2.44	2.47	2.45	0.02	3.05 ± 0.39
spy49_1416	scrB	Sucrose-6-phosphate hydrolase	1.67	2.00	1.83	0.23	NT
spy49_1417	scrR	Putative sucrose operon repressor	1.96	1.96	1.96	0.00	1.48 ± 0.62
spy49_1444c	cppA	Putative putative C3-degrading proteinase	1.65	1.63	1.64	0.02	NT
spy49_1782		Hypothetical protein	1.65	1.71	1.68	0.04	NT

^aGenes are listed according to the genomic location of the ORFs annotated in the GAS serotype M49 strain NZ131 and are considered differentially expressed if the log₂ of the fold change was ≤−1.58 or ≥1.58. Data have been deposited in the NCBI Gene Expression Omnibus (GEO) database under accession number GSE30397.

^bOnly significant values are shown (P ≤ 0.05). NT, not tested.