TABLE 4.

Crucial ORF candidates and differential expression for in vivo survival

S. intermedius TYG1620 genome annotation					Fold expression by RNA-seq		No. of Tn insertion sites in vitroa
Locus tag identifier	Gene	Product	COGb	LPXTG motifc	Abscess/BHI, 6 h	Abscess/BHI, 24 h
SITYG_00320	purH	Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase	F		11.6		1
SITYG_00400	purE	Phosphoribosylaminoimidazole carboxylase catalytic subunit PurE	F		−3.2	−13.1	1
SITYG_00620		Putative D12 class N6 adenine-specific DNA methyltransferase	L		6.0		5
SITYG_00740		Putative endonuclease			3.8		4
SITYG_00760		Hypothetical protein			4.0		8
SITYG_00870		Putative cell wall anchor protein		LPXTG	4.2		7
SITYG_00920		Putative membrane protein	U		7.2		3
SITYG_01560d		Hypothetical protein			4.9		3
SITYG_02210		Hypothetical protein	M		3.4		1
SITYG_02610		Hypothetical protein	GEPR		3.5		2
SITYG_04200		ABC transporter, ATP-binding protein	V		3.5		4
SITYG_04440		Hypothetical protein			5.8		1
SITYG_06470	celR	Putative transcriptional regulator	K		4.4		2
SITYG_07100		ABC sugar transporter permease protein	G		6.6		1
SITYG_07110		ABC sugar transporter membrane spanning permease	G		5.3		3
SITYG_08430		Hypothetical protein	S		3.8		3
SITYG_08540		Hypothetical protein	R		3.1		2
SITYG_08620		Hypothetical protein			3.8		3
SITYG_08760		Putative ABC transporter ATPase	R		7.0		2
SITYG_09320	pmrB	Putative transport protein	GEPR		3.3		3
SITYG_10560		Putative RNase	S		4.2		4
SITYG_10670		Competence protein	R		5.5		2
SITYG_10740		Hypothetical protein			3.3		2
SITYG_10880		Putative conjugal transfer protein TraG			3.5		7
SITYG_10910		Putative cell wall anchor protein		LPXTG	3.8		7
SITYG_10960		DNA topoisomerase	L		3.3		5
SITYG_10980		Hypothetical protein			7.3		8
SITYG_11020		Hypothetical protein			3.7		8
SITYG_12930		Putative ABC transporter, ATP-binding protein	V		5.7		2
SITYG_13570	glgA	Glycogen synthase	G		3.5		2
SITYG_13990		Beta-galactosidase	G		3.4	−3.1	7
SITYG_14150		Hypothetical protein			<−188.6	<−222.0	1
SITYG_15350		Putative uridine phosphorylase			3.2		2
SITYG_16240		Hypothetical protein			5.1		2
SITYG_16560		Transposase	L		4.9		1
SITYG_18050	comYB	Competence protein ComYB	NU		3.7	−3.1	1
SITYG_19460		Cell division protein FtsK	D		6.6		2

^aNumber of Tn insertion sites in vitro in in vivo-attenuated TYG1620 Tn mutants in murine model of subcutaneous infection.

^bCOG, cluster of orthologous groups.

^cSee Fig. 3.

^dORF located in T7SS (Fig. 2C).