TABLE 2.

Mutations observed in Enterococcus genomes after culturing with individual phages^a

Enterococcus strain	Phage(s)	Mutated host gene	Locus ID	Mutation type	Exopolysaccharide locus	V587 locus tag (EPA only)	AA change
E. faecalis DP11	Ump, SDS1	NAD-dependent epimerase/dehydratase	HOCGOLEH_00595	SNP	Epa gene	EF_2165	G11V, G279E
E. faecalis DP11	Ump	Bacterial sugar transferase	HOCGOLEH_00585	Nonsense	EpaR	EF_2177	E249*
E. faecalis DP11	SDS2	TagF gene. glycerol glycerophosphotransferase	HOCGOLEH_00593	SNP	Epa gene		A113E
E. faecalis Yi6	Bop	Bacterial sugar transferase	UMS_01916	SNP, nonsense	EpaR	EF_2177	N705Y
E. faecalis Yi6	Bop	UTP-glucose-1-phosphate uridylyltransferase	UMS_01646	DEL			K22*
E. faecalis Yi6	Bop	UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1	UMS_01161	SNP			A210T
E. faecalis Yi6	Bop	Isoleucyl-tRNA synthetase	UMS_00984	DEL			W31*
E. faecalis Yi6	phiV12	30S ribosomal protein S7	UMS_00243	SNP			G82D
E. faecalis Yi6	phiV12	DNA-directed RNA polymerase subunit alpha	UMS_00275	SNP			G29V
E. faecalis B3286	Bop, phiV12	NAD-dependent epimerase/dehydratase	SQ1_02166	SNP, nonsense	Epa gene	EF_2165	A123E, Q204*
E. faecalis B3286	Bop	Glucose-1-phosphate thymidylyltransferase;	SQ1_02191	SNP	EpaE	EF_2194	R217C
E. faecalis B3286	Bop	Endonuclease III	SQ1_01204	SNP			A130V
E. faecalis B3286	phiV12	Bacterial sugar transferase	SQ1_02177	SNP	EpaR	EF_2177	Y336*
E. faecalis B3286	phiV12	ATP-dependent Clp protease ATP-binding subunit ClpE	SQ1_00765	SNP			I13F
E. faecalis TX2137	Bop	Epimerase/dehydratase	HMPREF9494_02361	SNP	EpaW	EF_2171	D229Y, G192V
E. faecalis TX2137	Bop	Phosphocarrier protein HPr	HMPREF9494_02513	SNP			V209L
E. faecalis TX2137	Bop, phiV12	Bacterial sugar transferase	HMPREF9494_02367	SNP	EpaR	EF_2177	R400C, G251R
E. faecalis TX2137	phiV12	DNA ligase (NAD+)	HMPREF9494_02501	SNP			A434E
E. faecium TX1330	Ben	DNA gyrase subunit A (EC 5.99.1.3)	HMPREF0352_0587	SNP			D116A
E. faecium TX1330	Ben	DNA-directed RNA polymerase beta' subunit (EC 2.7.7.6)	HMPREF0352_2730	SNP			A924V
E. faecium TX1330	Bob	Response regulator transcription factor	D3Y30_RS07660	SNP			E192K
E. faecium TX1330	Bop	Polysaccharide biosynthesis protein	D3Y30_RS11110	SNP			L222S
E. faecium TX1330	Bop, Ben, Bill, no phage	CpsD/CapB family tyrosine-protein kinase	D3Y30_RS11120	SNP	Yqw		P136S, P26Q, L62E
E. faecium TX1330	Carl, phiV12, no phage	Tyrosine protein kinase	D3Y30_RS11125	SNP	Yqw		A147T, V153A

^aEach row indicates an Enterococcus gene in which one or more mutations were observed when that Enterococcus strain was cultured with the indicated phage. When more than one phage is listed the mutation occurred separately for each phage host pair and the phages were not used in combinations, the phages were not used in combinations. Locus ids refer to the genomes listed in Table S2 of the supplemental material. SNP, single-nucleotide polymorphism; DEL, deletion.