High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes

Salvadori, G.; Junges, R.; Åmdal, H. A.; Chen, T.; Morrison, D. A.; Petersen, F. C.

doi:10.1186/s12864-018-4802-y

Table 3 S. mitis type strain and SK321 orthologues of S. pneumoniae late genes in response to CSP in C + Y_YB

From: High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes

	Function in competence	S. pneumoniae		S. mitis				Description
		ID	Mean fold-change	ID		Mean fold-change^c
		TIGR4^b	R6^d	NCTC12261^a	SK321^a	NCTC12261	SK321
SigX Core Orthologues [29]	DNA uptake and recombination	0023	10	0021	0342	1.4	2.3	DNA repair protein RadA; radA
		0978	16	1411	01508a^f	58.6	139.6	Competence protein; coiA
		1266	64	1607	0695	63.8	339.3	DNA protecting protein DprA; dprA
		1908	64	0826	1193	98.6	697.9	Single-strand binding protein family; ssbB
		1940	16	0916	1658	5.3	18.8	Protein RecA; recA
		2208	128	0765	1614	113.2	591.7	Competence protein ComFA; comFA
		2207	64	01089^f	00402^f	133.6	1167.9	Competence protein, putative; comFC
		1808	16	0438	1050	57.0	694.6	Type 4 prepilin peptidase; cilC, pilD
		0954	32	1388	0421	122.8	627.9	ComE operon protein 1; comEA
		0955	64	1389	0422	93.6	839.4	DNA internalization-related competence protein ComEC
		2047	64	0629	1267	78.3	218.4	Methyltransferase small domain superfamily
		2048	64	0630	1268	187.6	992.0	ComG operon protein 6
		2049	64	01214^f	1269	141.4	1016.1	Hypothetical protein; cglE
		2050	64	0631	1270	164.6	852.6	Competence protein
		2051	64	0632	1271	192.2	1027.7	Competence protein
		2052	64	0633	1272	162.5	1079.0	Competence protein CglB; comYB
		2053	64	0634	1273	146.1	929.8	Putative ABC transporter subunit ComYA; comYA
	Lysis	2201	64	0760	1609	134.5	458.5	Choline binding protein D; cbpD
	Unknown functions in competence	0021	10	0019	0340	1.2	1.6	Deoxyuridine 5′-triphosphate nucleotidohydrolase, dut
		1981	8	0563	1204	1.3	4.3	Competence-induced protein Ccs50; ccs50
		1980	8	01275^f	00562^f	1.5	3.9	CMP-binding factor; yhaM, cbf1
		2206	32	0764	1613	2.2	4.1	Ribosome-associated factor Y; yfiA
		0979	8	1412	0443	1.5	3.4	Oligopeptidase F; pepB
		0782	8	1288	0286	7.1	47.2	Conserved domain protein; pilC
		1088	32	1568	0646	167.3	297.6	DNA repair protein RadC; radC
		2044	-^e	0627	1265	1.6	4.5	Acetate kinase; ackA
		1941	32	0915	1657	21.7	55.3	Competence/damage-inducible protein CinA; cinA
Non-Core Orthologues	Unknown functions in competence	0024	8	0022	0343	1.4	2.4	Carbonic anhydrase
		0025	4	0023	0344	1.3	2.2	Membrane protein, putative
		0031	16	00941^f	0345	6.7	1.2	Hypothetical protein
		0030	32	0025	0346	6.6	26.1	Competence-induced protein; Ccs16
		0029	4	0026	0347	5.0	1.9	Conserved hypothetical protein
		2045	8	0628	1266	3.3	19.8	Adenine-specific methyltransferase
		2197	16	0757	1606	3.7	86.4	ABC transporter substrate-binding protein
		2198	16	0758	1607	3.0	118.7	ABC transporter, permease protein
		2199	4	0759	1608	3.7	92.9	Conserved hypothetical protein
		1939	16	0917	1659	4.4	10.8	DNA-damage-inducible protein
		0980	6	1413	0444	1.7	3.9	O-methyltransferase family protein
		0981	4	1414	0445	1.3	2.7	Foldase protein PrsA
		1072	8	1421	0451	1.4	2.7	DNA primase
		1073	8	1422	0452	1.3	3.1	RNA polymerase sigma factor RpoD
		1074	8	1423	0453	1.3	3.0	N-6 Adenine-specific DNA methylase YitW
		0201	8	0853	1482	3.2	13.5	Competence-induced protein Ccs4; ccs4

^aGene number and product from HOMD
^bGene number and product from [51]
^cMean fold-change induction of CSP in S. mitis type strain and SK321 obtained by transcriptome analysis
^dExpression pattern during response the of S. pneumoniae to CSP pheromone [9]
^eNo upregulation detected by [9]
^fGene number according to PROKKA annotation [52]

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ISSN: 1471-2164

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