TABLE 1.

Differential gene expression detected by transcriptome sequencing in the D39s relative to the D39ΔfabT mutant^a

Regulation status in D39ΔfabT and gene no.b	Gene	Description	Log2 fold change	P valuec
Up
SPD_0140		ABC transporter ATP-binding protein	1.56	0.019
SPD_0185	cls	Cardiolipin synthase	0.72	0.008
SPD_0201	rpmC	50S ribosomal protein L29	0.65	0.046
SPD_0267		NCS2 family permease	0.63	0.012
SPD_0350	vraT	Cell wall-active antibiotic response protein	0.82	0.013
SPD_0351	vraS	Sensor histidine kinase	0.94	0.002
SPD_0354		DNA alkylation repair protein	1.16	0.032
SPD_0378	fabM	Enoyl-CoA hydratase	1.66	0.000
SPD_0380	fabH	Ketoacyl-ACP synthase III	0.73	0.000
SPD_0382	fabK	Enoyl-[acyl-carrier-protein] reductase FabK	2.05	0.000
SPD_0383	fabD	ACP S-malonyltransferase	1.77	0.000
SPD_0384	fabG	3-oxoacyl-[acyl-carrier-protein] reductase	1.70	0.000
SPD_0385	fabF	Beta-ketoacyl-ACP synthase II	1.76	0.000
SPD_0386	accB	Acetyl-CoA carboxylase biotin carboxyl carrier protein	1.79	0.000
SPD_0387	fabZ	3-Hydroxyacyl-ACP dehydratase FabZ	1.63	0.000
SPD_0388	accC	Acetyl-CoA carboxylase biotin carboxylase subunit	2.00	0.000
SPD_0389	accD	Acetyl-CoA carboxylase carboxyltransferase subunit beta	2.04	0.000
SPD_0390	accA	Acetyl-CoA carboxylase carboxyl transferase subunit alpha	2.13	0.000
SPD_0391	briC	Biofilm-regulating peptide BriC	1.19	0.004
SPD_0392		Hypothetical protein	0.87	0.031
SPD_0452	psrA d	Tyrosine-type DNA invertase PsrA	3.03	0.000
SPD_0453	hsdS	Restriction endonuclease subunit S	2.93	0.000
SPD_0501	licT	Transcription antiterminator Lict	1.95	0.000
SPD_0502		PTS glucose transporter subunit IIA	1.67	0.000
SPD_0503	bglA-2	6-Phospho-beta-glucosidase	1.69	0.000
SPD_0646		DegV family protein	1.49	0.000
SPD_0670		VanZ family protein	0.62	0.042
SPD_0671		ABC transporter ATP-binding protein	0.80	0.002
SPD_0684	bioY	Biotin transporter BioY	2.25	0.000
SPD_0688		ABC transporter permease	0.61	0.020
SPD_0691		PadR family transcriptional regulator	0.71	0.014
SPD_0703		DUF3270 domain-containing protein	1.31	0.020
SPD_0745	plsY	Glycerol-3-phosphate 1-O-acyltransferase PlsY	1.20	0.000
SPD_0772	pfkB	1-Phosphofructokinase	0.86	0.002
SPD_0858	mutM	DNA-formamidopyrimidine glycosylase	1.21	0.002
SPD_0859	coaE	Dephospho-CoA kinase	1.24	0.007
SPD_0860	pmrA	Multidrug efflux MFS transporter PmrA	1.16	0.019
SPD_0888	adcAII	Zinc-binding lipoprotein AdcAII	0.81	0.000
SPD_0889	phtD	Pneumococcal histidine triad protein PhtD	0.79	0.000
SPD_0890	phtE	Pneumococcal histidine triad protein PhtE	1.51	0.000
SPD_0913		DUF1002 domain-containing protein	1.77	0.014
SPD_0916	piaB	Iron ABC transporter permease	1.39	0.003
SPD_0917	piaC	Iron ABC transporter permease	1.38	0.008
SPD_0918	piaD	ABC transporter ATP-binding protein	1.20	0.015
SPD_1037	phtB	Pneumococcal-type histidine triad protein	0.69	0.008
SPD_1049	lacT	Transcription antiterminator	1.92	0.016
SPD_1164	cdd-2	Cytidine deaminase	2.18	0.000
SPD_1165		Phosphatidylglycerophosphatase A	1.30	0.000
SPD_1166		Hypothetical protein	1.34	0.000
SPD_1167	appD	ABC transporter ATP-binding protein	1.43	0.000
SPD_1168	appC	ABC transporter permease	1.54	0.000
SPD_1169	appB	ABC transporter permease	1.54	0.000
SPD_1170	appA	ABC transporter substrate-binding protein	1.16	0.007
SPD_1171		Cyclically permuted mutarotase family protein	1.30	0.000
SPD_1264		ABC transporter ATP-binding protein	1.35	0.015
SPD_1266		Energy-coupling factor transporter transmembrane protein EcfT	1.48	0.016
SPD_1267		ABC transporter ATP-binding protein	1.32	0.003
SPD_1276		EamA family transporter	0.91	0.004
SPD_1277		Serine hydrolase	0.79	0.013
SPD_1490		YesL family protein	1.29	0.016
SPD_1492	yjgK	Protein YjgK, linked to biofilm formation	1.71	0.003
SPD_1628	xpt	Xanthine phosphoribosyltransferase	1.11	0.003
SPD_1629	pbuX	Xanthine permease	1.13	0.001
SPD_2043	pcsB	Secreted antigen GbpB/SagA/PcsB, putative peptidoglycan hydrolase	1.41	0.033
SPD_2068	htrA	Serine protease, DegP/HtrA	1.48	0.012
Down
SPD_0004	ychF	Redox-regulated ATPase YchF	–0.59	0.037
SPD_0024	purA	Adenylosuccinate synthase	–0.55	0.019
SPD_0033	prsA	Ribose-phosphate diphosphokinase	–0.84	0.002
SPD_0063	strH	Beta-N-acetylhexosaminidase	–0.67	0.037
SPD_0074		Nucleoside phosphorylase	–0.74	0.015
SPD_0079		Hypothetical protein	–0.79	0.022
SPD_0098		Glycosyltransferase family 2 protein	–0.63	0.009
SPD_0340	rnpB	RNase P RNA component class B	–0.66	0.003
SPD_0369	zapA	Cell division protein ZapA	–0.68	0.010
SPD_0373	ahpD	Alkyl hydroperoxide reductase AhpD	–1.55	0.000
SPD_0379	fabT	MarR family transcriptional regulator	–15.50	0.000
SPD_0422		Hypothetical protein	–0.98	0.005
SPD_0423	xylR	Xylose repressor protein	–0.69	0.008
SPD_0450	hsdS	Restriction endonuclease subunit S	–3.07	0.000
SPD_0495		DUF3883 domain-containing protein	–0.74	0.032
SPD_0534	estA	Esterase family protein	–0.66	0.005
SPD_0558	prtA	Serine protease PrtA precursor	–1.19	0.005
SPD_0582		DUF3042 family protein	–0.99	0.032
SPD_0610		Hypothetical protein	–2.67	0.000
SPD_0611		Hypothetical protein	–2.17	0.002
SPD_0612		Hypothetical protein	–1.94	0.001
SPD_0613		Hypothetical protein	–1.64	0.001
SPD_0614		ABC transporter ATP-binding protein	–1.71	0.000
SPD_0637		lactoylglutathione lyase	–1.21	0.005
SPD_0649	upp	Uracil phosphoribosyltransferase	–0.96	0.000
SPD_0700	pepN	M1 family metallopeptidase	–0.59	0.034
SPD_0718		YkuJ family protein	–1.13	0.002
SPD_0754		DUF2969 domain-containing protein	–0.72	0.039
SPD_0853	lytB	Endo-beta-N-acetylglucosaminidase	–2.67	0.000
SPD_0957	dnaG	DNA primase	–0.81	0.000
SPD_0958	rpoD	RNA polymerase sigma factor RpoD	–0.69	0.001
SPD_0959		Metal-sulfur cluster assembly factor	–0.85	0.012
SPD_0997	hup	HU family DNA-binding protein	–0.87	0.003
SPD_1141	uraA	Uracil transporter	–2.52	0.002
SPD_1212	ywbD	Putative ribosomal RNA large subunit methyltransferase YwbD	–0.58	0.033
SPD_1274	guaA	Glutamine-hydrolyzing GMP synthase	–0.53	0.032
SPD_1295		Hemolysin III family protein	–0.80	0.022
SPD_1431	gtrB	Bactoprenol glucosyl transferase	–0.80	0.007
SPD_1461	psaB	Manganese ABC transporter, ATP-binding protein	–1.98	0.009
SPD_1462	psaC	Manganese ABC transporter, permease protein, putative	–1.97	0.006
SPD_1463	psaA	Metal ABC transporter substrate-binding lipoprotein/adhesin PsaA	–1.88	0.022
SPD_1468	gpmA	Phosphoglycerate mutase	–0.98	0.001
SPD_1483	murF	UDP-N-acetylmuramoyl-tripeptide–d-alanyl-d-alanine ligase	–0.78	0.000
SPD_1548	gmk	Guanylate kinase	–0.48	0.042
SPD_1581		tRNA-Lys-CUU	–1.11	0.000
SPD_1594		XRE family transcriptional regulator	–0.69	0.009
SPD_1595		Hypothetical protein	–0.76	0.014
SPD_1649	piuB	Iron-compound ABC transporter, Permease protein	–2.13	0.011
SPD_1650	piuC	Iron-compound ABC transporter, permease protein	–4.54	0.000
SPD_1651	piuD	Iron-compound ABC transporter, ATP-binding protein	–2.98	0.000
SPD_1652	piuA	Iron-compound ABC transporter, iron-compound-binding protein	–2.88	0.018
SPD_1775	lysA	Diaminopimelate decarboxylase	–0.71	0.024
SPD_1790	rpmH	50S ribosomal protein L34	–0.82	0.048
SPD_1899		Gamma-glutamyl-gamma-aminobutyrate hydrolase family protein	–1.35	0.022
SPD_1903	mutS	DNA mismatch repair protein MutS	–0.54	0.041
SPD_1922	hipO	N-acetyldiaminopimelate deacetylase	–0.59	0.043
SPD_1923	dapD	2,3,4,5-Tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase	–0.85	0.004
SPD_1926	tyrS	Tyrosine-tRNA ligase	–1.07	0.002
SPD_1927	ctpC	Heavy metal translocating P-type ATPase	–0.96	0.000
SPD_1931		Membrane protein	–0.74	0.020
SPD_1984	ybbK	Putative stomatin/prohibitin-family membrane protease subunit YbbK	–1.09	0.003
SPD_2018		Isoprenylcysteine carboxyl methyltransferase family protein	–0.80	0.033
SPD_2055	guaB	IMP dehydrogenase	–0.86	0.003

^aLog2 fold change in gene expression as assessed by RNA-seq.

^bThe reference genome under GenBank accession numbers NC_008533.2 and CP027540.1.

^cAdjusted P values, P values were adjusted using the Benjamini and Hochberg method.

^dSpnD39III type I restriction-modification system genes are indicated in bold.