Table 1 List of genes related to the stringent response that are dysregulated in biofilms treated with subinhibitory doses of phiIPLA-RODI compared to untreated biofilms according to RNA-seq.

From: Low-level predation by lytic phage phiIPLA-RODI promotes biofilm formation and triggers the stringent response in Staphylococcus aureus

Gene ID	Gene name	Gene product	FC
SAOUHSC_00005	gyrB	DNA gyrase subunit B	−2.89
SAOUHSC_00006	gyrA	DNA gyrase subunit A	−3.92
SAOUHSC_00121		Capsular polysaccharide synthesis enzyme O-acetyl transferase Cap5H, putative	2.03
SAOUHSC_00187	pflB	Formate acetyltransferase	−4.57
SAOUHSC_00188	pflA	Pyruvate formate-lyase-activating enzyme	−5.52
SAOUHSC_00350	rpsR	30 S ribosomal protein S18	−2.69
SAOUHSC_00471	glmU	Bifunctional protein GlmU	−2.73
SAOUHSC_00474	rplY	50 S ribosomal protein L25	−2.06
SAOUHSC_00528	rpsG	30 S ribosomal protein S7	−2.07
SAOUHSC_00733	hisC	Histidinol-phosphate aminotransferase	3.53
SAOUHSC_00780	uvrA	UvrABC system protein A	−2.07
SAOUHSC_00796	pgk	Phosphoglycerate kinase	−2.90
SAOUHSC_00797	tpiA	Triosephosphate isomerase	−3.32
SAOUHSC_00799	eno	Enolase	−4.31
SAOUHSC_00802		Carboxylesterase, putative	−2.11
SAOUHSC_00818	nuc	Thermonuclease	5.72
SAOUHSC_00933	trpS	Tryptophan–tRNA ligase	2.25
SAOUHSC_00994	atl	Bifunctional autolysin	5.42
SAOUHSC_01002	qoxA	Probable quinol oxidase subunit 2	−2.54
SAOUHSC_01092	pheS	Phenylalanine–tRNA ligase alpha subunit	−2.04
SAOUHSC_01093	pheT	Phenylalanine–tRNA ligase beta subunit	−3.45
SAOUHSC_01164	pyrR	Bifunctional protein PyrR	−2.25
SAOUHSC_01168	pyrC	Dihydroorotase	−4.79
SAOUHSC_01207	ffh	Signal recognition particle protein	−2.50
SAOUHSC_01216	sucC	Succinyl-CoA ligase [ADP-forming] subunit beta	−2.80
SAOUHSC_01247	rbfA	Ribosome-binding factor A	−4.19
SAOUHSC_01276	glpK	Glycerol kinase	−2.56
SAOUHSC_01320	hom	Homoserine dehydrogenase	3.25
SAOUHSC_01395	asd	Aspartate-semialdehyde dehydrogenase	4.35
SAOUHSC_01396	dapA	4-hydroxy-tetrahydrodipicolinate synthase	4.40
SAOUHSC_01397	dapB	4-hydroxy-tetrahydrodipicolinate reductase	2.81
SAOUHSC_01466	recU	Holliday junction resolvase RecU	−3.02
SAOUHSC_01504		Ferredoxin, putative	−3.37
SAOUHSC_01585	srrB	Sensor protein SrrB	−3.29
SAOUHSC_01586	srrA	Transcriptional regulatory protein SrrA	−5.06
SAOUHSC_01601		Alpha-glucosidase, putative	−2.76
SAOUHSC_01668	era	GTPase Era	−2.96
SAOUHSC_01681	prmA	Ribosomal protein L11 methyltransferase	−13.21
SAOUHSC_01715	udk	Uridine kinase	−2.38
SAOUHSC_01737	aspS	Aspartate–tRNA ligase	−2.95
SAOUHSC_01742	rsh	GTP pyrophosphokinase	4.91
SAOUHSC_01755	rpmA	50 S ribosomal protein L27	−3.58
SAOUHSC_01767	valS	Valine–tRNA ligase	−3.46
SAOUHSC_01771	hemL1	Glutamate-1-semialdehyde 2,1-aminomutase 1	−2.90
SAOUHSC_01772	hemB	Delta-aminolevulinic acid dehydratase	−2.71
SAOUHSC_01776	hemA	Glutamyl-tRNA reductase	−2.06
SAOUHSC_01784	rplT	50 S ribosomal protein L20	−2.31
SAOUHSC_01818	ald2	Alanine dehydrogenase 2	−2.89
SAOUHSC_01886	ribH	6,7-dimethyl-8-ribityllumazine synthase	−10.04
SAOUHSC_01887	ribBA	Riboflavin biosynthesis protein	−7.35
SAOUHSC_01889	ribD	Riboflavin biosynthesis protein	−4.03
SAOUHSC_01961	hemH	Ferrochelatase	−2.32
SAOUHSC_01972	prsA	Foldase protein PrsA	−3.26
SAOUHSC_02254	groEL	60 kDa chaperonin	−4.48
SAOUHSC_02340	atpC	ATP synthase epsilon chain	−2.87
SAOUHSC_02341	atpD	ATP synthase subunit beta	−2.87
SAOUHSC_02349	atpE	ATP synthase subunit c	−2.38
SAOUHSC_02350	atpB	ATP synthase subunit a	−2.31
SAOUHSC_02477	rpsI	30 S ribosomal protein S9	−2.08
SAOUHSC_02505	rplP	50 S ribosomal protein L16	−2.02
SAOUHSC_02506	rpsC	30 S ribosomal protein S3	−2.11
SAOUHSC_02509	rplB	50 S ribosomal protein L2	−2.72
SAOUHSC_02510	rplW	50 S ribosomal protein L23	−2.71
SAOUHSC_02511	rplD	50 S ribosomal protein L4	−2.65
SAOUHSC_02536	moaA	Cyclic pyranopterin monophosphate synthase	−2.81
SAOUHSC_02537	mobA	Probable molybdenum cofactor guanylyltransferase	−3.16
SAOUHSC_02635	tcaA	Membrane-associated protein TcaA	−2.32
SAOUHSC_02669	sarZ	HTH-type transcriptional regulator SarZ	4.75
SAOUHSC_02696	fmhA	FmhA protein	2.68
SAOUHSC_02834	srtA	Sortase	2.95
SAOUHSC_02850	cidB	Holin-like protein CidB	−2.28
SAOUHSC_02965	arcC2	Carbamate kinase 2	−6.75
SAOUHSC_02969	arcA	Arginine deiminase	−5.89
SAOUHSC_03002	zwf	Poly-beta-1,6-N-acetyl-D-glucosamine synthase	3.16
SAOUHSC_03002	icaA	Poly-beta-1,6-N-acetyl-D-glucosamine synthase	3.16
SAOUHSC_03055	rpmH	50 S ribosomal protein L34	−3.07

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Table 1 List of genes related to the stringent response that are dysregulated in biofilms treated with subinhibitory doses of phiIPLA-RODI compared to untreated biofilms according to RNA-seq.

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