Table 3.

Genes upregulated in the LMD-9 MecA⁻ strain compared to WT strain LMD-9 grown under THBG conditions

Category and locus tag in LMD-9	Gene	Descriptione	Strand	FCa		Late com gene in S. pneumoniaeb	Presence of:
				MecA− strain	ComX− strain		Essential com in S. pneumoniaec	ComX boxd
MecA-regulated genes shared with the late com regulon
STER_0406	comFA	Late competence protein required for DNA uptake	+	1.6	7.2	SP_2208	Y	Y
STER_0407	comFC	Late competence protein	+	1.9	7.6	SP_2207	Y
STER_0488	coiA	Competence protein, transcription factor	+	27.0	42.0	SP_0978	Y	Y
STER_0489	pepB	Oligopeptidase	+	2.4	18.9	SP_0979
STER_0922	dprA	DNA-processing protein, Smf family	+	31.3	72.2	SP_1266	Y	Y
STER_0923	topA	DNA topoisomerase I	+	2.6	29.9
STER_1029		Pseudo		1.8	11.3
STER_1030		Hypothetical protein	−	1.8	13.4
STER_1031		Pseudo		1.6	8.7
STER_1519	murZ	UDP-N-Acetylglucosamine 1-carboxyvinyltransferase	−	2.0	6.8
STER_1520	comEC	Late competence protein required for DNA uptake	−	22.1	23.2	SP_0955	Y
STER_1521	comEA	Late competence protein required for DNA binding and uptake	−	15.1	10.7	SP_0954	Y	Y
STER_1818		Hypothetical protein	+	1.5	7.1
STER_1819		Cytidine/deoxycytidylate deaminase family protein, putative	−	1.6	16.3
STER_1820		Hypothetical protein	−	2.3	21.1
STER_1821	ssbA	Single-strand DNA-binding protein	−	1.7	23.3	SP_1908	Y	Y
STER_1834	ackA	Acetate kinase	−	3.4	25.9
STER_1835		Hypothetical protein	−	8.4	72.6	SP_2045
STER_1836		Hypothetical protein	−	62.0	181.4	SP_2047	Y
STER_1837		Competence protein, putative	−	67.2	163.2	SP_2048
STER_1838		Pseudo		77.0	190.4
STER_1839	comGD	Competence protein	−	72.8	151.3	SP_2050	Y
STER_1840	comGC	Late competence protein, exogenous DNA-binding protein	−	83.5	203.3	SP_2051	Y
STER_1841	comGB	Late competence protein, ABC transporter subunit	−	77.4	147.3	SP_2052	Y
STER_1842	comGA	Late competence protein, ABC transporter subunit	−	46.7	50.0	SP_2053	Y	Y
STER_1677		ABC transporter, permease protein	−	1.8	2.8
STER_1678		ABC-type multidrug transport system, ATPase component	−	1.8	2.7
Unique MecA-regulated genes
STER_0596		Pyridine nucleotide-disulfide oxidoreductase	+	1.9	<1.5
STER_0588		Hypothetical protein	+	2.3	<1.5
STER_0870	ptpS	6-Pyruvoyl tetrahydrobiopterin synthase	+	1.5	<1.5
STER_0871		Putative coenzyme PQQ synthesis protein	+	1.6	<1.5
STER_0872		7-Cyano-7-deazaguanine reductase	+	1.6	<1.5
STER_1022		High-affinity Fe2+/Pb2+ permease	−	4.4	<1.5
STER_1023		Hypothetical protein	−	4.4	<1.5
STER_1024		Hypothetical protein	−	5.3	<1.5
STER_1025		ABC-type Fe3+-hydroxamate transport system, periplasmic component	−	7.3	<1.5
STER_1026	fatA	ABC-type spermidine/putrescine transport system, ATPase component	−	7.7	<1.5
STER_1027	fatC	ABC-type Fe3+-siderophore transport system, permease component	−	7.4	<1.5
STER_1028	fatD	ABC-type Fe3+-siderophore transport system, permease component	−	6.8	<1.5
STER_1257	ldh	l-Lactate dehydrogenase	+	1.8	<1.5
STER_1601		Hypothetical protein	+	1.9	<1.5
STER_1602		Pseudo		1.8	<1.5
STER_1639		Hypothetical protein	−	1.5	<1.5
STER_1683		Hypothetical protein	−	3.4	<1.5
STER_1684		Response regulator	−	3.6	<1.5
STER_1709	scrK	Fructokinase	−	1.6	<1.5
STER_1710	scrA	Sucrose PTS, enzyme IIBCA	−	2.0	<1.5

^aMean absolute fold change (FC) with a cutoff value of ≥1.5 and a P value of <0.05 for the LMD-9 MecA⁻ strain (WT versus CB0052) and the LMD-9 ComX⁻ strain (WT versus CB003).

^bLate com genes identified in S. pneumoniae TGIR4 (41). Orthologous genes with an identity of >40% were identified by BlastP.

^cLate com genes identified in S. pneumoniae TGIR4 as being essential for competence (41). Y, presence of an orthologous gene in LMD-9.

^dPresence (Y) of a conserved ComX box ([T/A]NCGAAT[A/G]) in the upstream intergenic region.

^ePseudo, pseudogene; PQQ, pyrroloquimoline quinone; PTS, phosphotransferase system.