TABLE 4.

CcpA binding sites identified by ChIP‐seq analysis and associated genes

CBSa	Bound by WT	Bound by V301A	cre	cre locationb	cre sequence	Locus tagc	Gene	Annotation	COG	Regulated by CcpA	HPr‐dependency
1	Yes	Yes	Yes	Prom	AAAGAAAGCGGTTTCA	M5005_Spy_0039	adh2	Bifunctional acetaldehyde‐CoA/alcohol dehydrogenase	C	Yes	Semi dependent
2	Yes	Yes	Yes	Prom	ACAGAAAACGATTTCA	M5005_Spy_0094	ackA	Acetate kinase	F	Yes	Independent
3	Yes	No	Yes	ORF	ATGGTGGCGTTTTCTT	M5005_Spy_0128	ntpE	V‐type ATP synthase subunit E	C	Yes	Independent
4	Yes	Yes	Yes	Prom	AACGAAAACCTTTTCA	M5005_Spy_0180	–	Hypothetical protein	D	No	NA
4	Yes	Yes	Yes	Prom	AACGAAAACCTTTTCA	M5005_Spy_0185	pgi	pgi	G	No	NA
5	Yes	No	Yes	Prom	TTGAAAGCGCTTTATT	M5005_Spy_0212	–	N‐acetylmannosamine‐6‐phosphate 2‐epimerase	G	Yes	Independent
6	Yes	Yes	Yes	Prom	AAAGAAAGCCCTTTCC	M5005_Spy_0233	plr	Aldehyde dehydrogenase	G	No	NA
7	Yes	Yes	Yes	Prom	AATGTAAGCGCTAACAAAAT	M5005_Spy_0339	exoA	Exodeoxyribonuclease	L	Yes	Independent
7	Yes	Yes	Yes	Prom	AATGTAAGCGCTAACAAAAT	M5005_Spy_0340	lctO	L‐lactate oxidase	C	Yes	Semi dependent
8	Yes	Yes	Yes	ORF	TAGGAAGCGTTTTCTT	M5005_Spy_0341	prtS	Peptidase S8	O	Yes	Independent
9	Yes	No	Yes	ORF	GTGCAAGCGCTTTGAT	M5005_Spy_0362	gcaD	Glucosamine‐1‐phosphate acetyltransferase	M	No	NA
10	Yes	No	No	–	–	M5005_Spy_0416		Glutamine cyclotransferase	O	No	NA
10	Yes	No	No	–	–	M5005_Spy_0417	pcp	Pyrrolidone‐carboxylate peptidase	O	No	NA
11	Yes	No	No	–	–	M5005_Spy_0417	pcp	Pyrrolidone‐carboxylate peptidase	O	No	NA
12	Yes	No	Yes	Prom	TTGAAAACTTTTTCAA	M5005_Spy_0424	ccpA	Catabolite control protein A	K	Yes	Independent
13	Yes	No	No	–	–	M5005_Spy_0495	lysS	Lysine‐‐tRNA ligase	J	No	NA
13	Yes	No	No	–	–	M5005_Spy_0496		Haloacid dehalogenase	S	No	NA
14	Yes	No	No	–	–	M5005_Spy_0504	pepF	Oligoendopeptidase F	E	No	NA
15	Yes	Yes	Yes	ORF	TTTGGGAACGATTTCTCAAG	M5005_Spy_0771	–	CRISPR‐associated endonuclease Cas2	L	No	NA
16	Yes	Yes	Yes	Prom	AAATAAAGCGCTTACT	M5005_Spy_0505	ppc	Phosphoenolpyruvate carboxylase	H	Yes	Fully dependent
17	Yes	Yes	Yes	Prom	GAGAAAACGTTTTAGT	M5005_Spy_0512	–	Sugar phosphate phosphatase	S	Yes	Fully dependent
18	Yes	No	Yes	Prom	TTGACACCGTTTTCAT	M5005_Spy_0533	–	Hypothetical protein	S	Yes	Independent
18	Yes	No	Yes	Prom	TTGACACCGTTTTCAT	M5005_Spy_0534	–	Acetoin reductase	IQ	Yes	Semi dependent
19	Yes	No	Yes	ORF	GAAGATATCGCTTCTA	M5005_Spy_0556	eno	Phosphopyruvate hydratase	F	No	NA
20	Yes	No	Yes	Prom	TATTATATCGATTTCT	M5005_Spy_0555	–	Hypothetical protein	S	No	NA
20	Yes	No	Yes	Prom	TATTATATCGATTTCT	M5005_Spy_0556	eno	Phosphopyruvate hydratase	F	No	NA
21	Yes	Yes	Yes	Prom	AAGAAAGGGTTTACAT	M5005_Spy_0562	sagA	Streptolysin S family bacteriocin		Yes	Semi dependent
22	Yes	No	Yes	ORF	ATGGAAGCTTTTTCAG	M5005_Spy_0622	–	Alkaline phosphatase	M	No	NA
22	Yes	No	Yes	ORF	ATGGAAGCTTTTTCAG	M5005_Spy_0625	aroF	Chorismate synthase	E	No	NA
23	Yes	No	Yes	ORF	GTGAAGGGTTTATCAT	M5005_Spy_0772	–	Type II‐A CRISPR‐associated protein Csn2	S	No	NA
24	Yes	No	No	–	–	M5005_Spy_0778	msrB	Peptide‐methionine (R)‐S‐oxide reductase	O	No	NA
25	Yes	Yes	Yes	ORF	GAAGATAACGATTTCA	M5005_Spy_0817	dacA1	D‐alanyl‐D‐alanine carboxypeptidase	M	No	NA
26	Yes	No	Yes	ORF	TTGTAAGCGCTACCGA	M5005_Spy_0823	folQ	Dihydroneopterin aldolase	H	No	NA
27	Yes	Yes	Yes	Prom	AAGAAAGGGTTTTCAA	M5005_Spy_0834	–	Alcohol dehydrogenase	E	Yes	Semi dependent
27	Yes	Yes	Yes	Prom	AAGAAAGGGTTTTCAA	M5005_Spy_0835	–	Acid phosphatase/phosphotransferase	S	Yes	Semi dependent
28	Yes	No	Yes	Prom	ACTGATAACGCTTCCAA	M5005_Spy_0873	ldh	L‐lactate dehydrogenase	C	No	NA
28	Yes	No	Yes	Prom	ACTGATAACGCTTCCAA	M5005_Spy_0874	gyrA	DNA gyrase subunit A	L	No	NA
29	Yes	No	No	–	–	M5005_Spy_0925	rnhB	Hypothetical protein	F	No	NA
30	Yes	Yes	Yes	Prom	CTTGAAACCGCTTGCT	M5005_Spy_0934	‐	Lipoate‐‐protein ligase	H	Yes	Fully dependent
31	Yes	No	Yes	Prom	AATGAAAGCGTTTATA	M5005_Spy_0938	pgmA	Phosphoglucomutase	G	Yes	Semi dependent
32	Yes	No	No	–	–	M5005_Spy_0938	pgmA	Phosphoglucomutase	G	Yes	Semi dependent
33	Yes	No	No	–	–	M5005_Spy_0938	pgmA	Phosphoglucomutase	G	Yes	Semi dependent
34	Yes	Yes	Yes	ORF	TAAGATACCGCTTGCA	M5005_Spy_1055	glgP	Maltodextrin phosphorylase	G	Yes	Independent
34	Yes	Yes	Yes	ORF	TAAGATACCGCTTGCA	M5005_Spy_1058	malE	Maltose/maltodextrin‐binding protein	G	Yes	Independent
35	Yes	Yes	Yes	Prom	CTGCAAGCGGTTGCAT	M5005_Spy_1057	malR	LacI family transcriptional regulator	K	Yes	Independent
35	Yes	Yes	Yes	Prom	CTGCAAGCGGTTGCAT	M5005_Spy_1058	malE	Maltose/maltodextrin‐binding protein	G	Yes	Independent
36	Yes	Yes	Yes	Prom	ATCGTAATCGCTTTCA	M5005_Spy_1067	malX	Sugar ABC transporter substrate‐binding protein	G	Yes	Semi dependent
37	Yes	Yes	Yes	Prom	TTAGAAAACGCTTTCT	M5005_Spy_1083	bglG	Transcription antiterminator BglG	G	Yes	Semi dependent
38	Yes	Yes	Yes	ORF	CTAAAAGCGTTTTCTC	M5005_Spy_1096	–	Thioesterase	Q	No	NA
39	Yes	No	Yes	Prom	CATGATAACCCTTACA	M5005_Spy_1122	nrdH	NrdH‐redoxin	O	Yes	Independent
39	Yes	No	Yes	Prom	CATGATAACCCTTACA	M5005_Spy_1121	ptsH	Phosphocarrier protein HPr	G	Yes	NA
40	Yes	Yes	Yes	Prom	CAAGAAATCGCTTTCT	M5005_Spy_1235	–	Phosphomannomutase	G	Yes	Semi dependent
41	Yes	No	Yes	ORF	CAGAAAACTCTTTCTT	M5005_Spy_1250	ftsA	Cell division protein FtsA	D	No	NA
42	Yes	No	Yes	Prom	ATGGAATCGCTTTCTA	M5005_Spy_1258	–	Hypothetical protein	S	Yes	Independent
43	Yes	No	Yes	ORF	ATCGTAAGCGCCTCCA	M5005_Spy_1265	–	Ribose operon repressor		No	NA
44	Yes	No	Yes	ORF	GTAAAATCTTTTTCTG	M5005_Spy_1272	–	Arginine:ornithine antiporter	S	Yes	Semi dependent
45	Yes	No	No	–	–	M5005_Spy_1274		N‐acetyltransferase	K	Yes	Semi dependent
46	Yes	No	No	–	–	M5005_Spy_1274		N‐acetyltransferase	K	Yes	Semi dependent
47	Yes	No	No	–	–	M5005_Spy_1274		N‐acetyltransferase	K	Yes	Semi dependent
48	Yes	Yes	Yes	Prom	TGAGTAATCGCTTACA	M5005_Spy_1275	arcA	Arginine deiminase	E	Yes	Semi dependent
48	Yes	Yes	Yes	Prom	TGAGTAATCGCTTACA	M5005_Spy_1277	ahrC.2	Arginine regulator	K	Yes	Semi dependent
49	Yes	Yes	Yes	ORF	CTGCAATCGTTTACTT	M5005_Spy_1319	–	RNA methyltransferase	J	No	NA
49	Yes	Yes	Yes	ORF	CTGCAATCGTTTACTT	M5005_Spy_1323	–	Hypothetical protein	L	No	NA
50	Yes	Yes	Yes	Prom	CTTGAAGCGCTTACTT	M5005_Spy_1328	–	YigZ family protein	S	Yes	Independent
50	Yes	Yes	Yes	Prom	CTTGAAGCGCTTACTT	M5005_Spy_1325	–	Ribosome‐associated factor Y	J	Yes	Fully dependent
51	Yes	No	No	–	–	M5005_Spy_1366		Penicillin‐binding protein 2X	M	No	NA
52	Yes	Yes	Yes	ORF	GAGAAAAGGATTTCAT	M5005_Spy_1367	ftsL	Cell division protein FtsL	D	No	NA
53	Yes	Yes	Yes	Prom	AAGTAAGCGTTTTCCT	M5005_Spy_1381	glpK	Glycerol kinase	F	Yes	Independent
54	Yes	No	No	–	–	M5005_Spy_1382		Hypothetical protein	T	Yes	Independent
55	Yes	Yes	Yes	Prom	CTGTAAGCGATTACTT	M5005_Spy_1387	–	2,5‐diketo‐D‐gluconic acid reductase	C	Yes	Independent
56	Yes	No	No	–	–	M5005_Spy_1448		Nuclease	S	No	NA
57	Yes	Yes	Yes	Prom	GTGAAAACGTTTTAAA	M5005_Spy_1477	–	NCS2 family permease	S	Yes	Semi dependent
57	Yes	Yes	Yes	Prom	GTGAAAACGTTTTAAA	M5005_Spy_1479	manL	PTS mannose transporter subunit EIIAB	G	Yes	Semi dependent
58	Yes	Yes	Yes	Prom	AAAGAAAACGTTTTCT	M5005_Spy_1496	phaB	Enoyl‐CoA hydratase	I	Yes	Independent
59	Yes	No	No	–	–	M5005_Spy_1497	dnaJ	Chaperone DnaJ	O	Yes	Fully dependent
60	Yes	No	Yes	Prom	AAAGAAAACACTTGCA	M5005_Spy_1503	–	Histidine phosphatase family protein	G	Yes	Independent
61	Yes	No	No	–	–	M5005_Spy_1513		Aminotransferase	E	No	NA
61	Yes	No	No	–	–	M5005_Spy_1514		Universal stress protein UspA	T	No	NA
62	Yes	Yes	Yes	Prom	TGGGAAAACGTTTCCT	M5005_Spy_1569	pfl	Formate acetyltransferase	C	Yes	Independent
63	Yes	No	No	–	–	M5005_Spy_1575	norA	MFS transporter	EGP	Yes	Fully dependent
64	Yes	No	Yes	Prom	TTTAAAGCTTTTTAA	M5005_Spy_1599	pgk	Phosphoglycerate kinase	F	No	NA
65	Yes	Yes	Yes	Prom	ATAAAAGCGTTATCTC	M5005_Spy_1624	–	Hypothetical protein		No	NA
66	Yes	Yes	Yes	ORF	AGAGAAACCGGTACCA	M5005_Spy_1627	salY	ABC transporter permease	V	No	NA
67	Yes	Yes	Yes	Prom	TGCGCAAGCGCTTGCA	M5005_Spy_1680	pulA	Pullulanase	G	No	NA
68	Yes	Yes	Yes	Prom	GATGCAATCGCTTGCA	M5005_Spy_1692	–	PTS maltose	G	Yes	Independent
69	Yes	Yes	Yes	ORF	GTGATAGCGCTATCTT	M5005_Spy_1734	speB	Streptopain	M	Yes	Independent
69	Yes	Yes	Yes	ORF	GTGATAGCGCTATCTT	M5005_Spy_1736	–	Hypothetical protein		Yes	Independent
70	Yes	No	Yes	Prom	TTGTAATCGTTTACAT	M5005_Spy_1746	–	PTS cellobiose transporter subunit IIA	G	Yes	Semi dependent
71	Yes	No	No	–	–	M5005_Spy_1758		Dipeptidase	M	Yes	Semi dependent
72	Yes	Yes	Yes	Prom	GTGAAAGCGTTATCGT	M5005_Spy_1758	–	Dipeptidase	M	Yes	Semi dependent
73	Yes	Yes	Yes	Prom	ATGTAAGCGTTATCTAA	M5005_Spy_1772	–	Glutamate formimidoyltransferase	E	Yes	Independent
73	Yes	Yes	Yes	Prom	ATGTAAGCGTTATCTAA	M5005_Spy_1770	hutI	Imidazolonepropionase	Q	Yes	Semi dependent
74	Yes	Yes	Yes	Prom	CATGAAAACGCCTCCA	M5005_Spy_1779	rpsB	ATP‐binding protein	T	Yes	Semi dependent
75	Yes	No	No	–	–	M5005_Spy_1807	argR2	Arginine repressor	K	Yes	Independent
76	Yes	Yes	Yes	ORF	ACAGATAACGCTTACT	M5005_Spy_1865	htrA	Serine protease	O	No	NA

Abbreviation: NA, not applicable.

^a CcpA binding site number

^b Prom, binding site located in noncoding promoter region upstream of ATG. ORF, binding site identified within coding region of gene.

^c Locus tag numbers are based on the MGAS5005 genome.