. 2016 Feb 5;7:87. doi: 10.3389/fmicb.2016.00087

Table 1.

Genes of Staphylococcus xylosus discussed in this study differentially expressed over time in meat.

Gene ID	Gene name	Description	Mean ratio of expression
			24 h	48 h	72 h
CELL DIVISION AND CELL LYSIS
Replication, recombination, repair, and transcription
SXYL_01165	dnaE	DNA polymerase III subunit alpha	2.6	3.5	2.6
SXYL_01799		DNA polymerase X family protein	2.4	2.6	2.0
SXYL_01529-30	parCE	DNA topoisomerase 4 subunit A, B	5.0^*	3.8^*	2.9^*
SXYL_00016	dnaB	Replicative DNA helicase	4.9	4.4	3.7
SXYL_01219	ruvB	Holliday junction ATP-dependent DNA helicase RuvB	4.2	3.4	2.5
SXYL_01659	recG	ATP-dependent DNA helicase RecG	3.8	4.0	2.6
SXYL_02129	recQ1	ATP-dependent DNA helicase RecQ	4.8	7.0	5.0
SXYL_01954	addA	ATP-dependent helicase/nuclease subunit A	4.0	3.4	2.4
SXYL_00005-06	gyrAB	DNA gyrase subunits A and B	3.7^*	3.9^*	2.8^*
SXYL_02427	mfd	Transcription-repair-coupling factor	5.8	6.9	4.2
SXYL_01583	mutS1	DNA mismatch repair protein MutS	3.6	4.2	2.9
SXYL_01798	mutS2	Endonuclease MutS2	3.2	4.8	3.5
SXYL_02373	fusA	Elongation factor G	3.5	2.4
SXYL_01273	lepA	Elongation factor 4	8.4	8.2	5.9
SXYL_00727	infA	Translation initiation factor IF-1	5.8	3.2	2.5
SXYL_01186	infC	Translation initiation factor IF-3	6.2	4.1	3.9
Nucleotides transport and metabolism
SXYL_02522-21	xpt, pbuX	Xanthine phosphoribosyltransferase, Xanthine permease	7.8^*	3.7^*	3.6^*
SXYL_01690	pyrP	Uracil permease	16.2	6.3	4.1
SXYL_02420	hpt	Hypoxanthine phosphoribosyltransferase	6.7	4.0	2.7
SXYL_00017	purA	Adenylosuccinate synthetase	13.2	8.6	5.0
SXYL_00796	pdp	Pyrimidine-nucleoside phosphorylase	2.0	2.8	2.5
SXYL_00821	upp	Uracil phosphoribosyltransferase	9.6	8.2	6.1
SXYL_01689-85	pyrBC, carAB, pyrF	UMP biosynthesis	7.8^*	5.0^*	2.9^*
SXYL_00807	pyrG	CTP synthase	5.7	5.2	4.3
Division
SXYL_01703	ftsA	Cell division protein FtsA	2.9	2.8	2.6
SXYL_01801	zapA	Cell division protein ZapA	2.7	2.2	2.2
SXYL_01704	divIB	Cell division protein DivIB	4.8	3.5	2.7
SXYL_00848		Cell division protein, FtsW/RodA/SpoVE family	4.1	2.6	2.0
SXYL_01212	mreD	Cell shape-determining protein MreD	3.2	3.0	2.4
SXYL_01651	smc	Chromosome partition protein Smc	3.5	3.6	2.2
SXYL_01699	sepF	Cell division protein sepF	0.3	0.2	0.3
SXYL_01710	mraZ	Protein MraZ	0.3	0.1	0.2
SXYL_00116	sceD2	Probable transglycosylase SceD 2	34.5	31.9	49.3
Peptidoglycan synthesis
SXYL_00822	mnaA	UDP-N-acetylglucosamine 2-epimerase	8.5	6.6	4.5
SXYL_01425	murG	UDP-N-acetylglucosamine-tr ansferase	2.4	2.9	2.3
SXYL_02467	sle1	N-acetylmuramoyl-L-alanine amidase Sle1	5.7	5.2	6.1
SXYL_01706-05	mraY, murD	Phospho-N-acetylmuramoyl-pentapeptide-transferase, UDP-N-acetylmuramoylalanine–D-glutamate ligase	8.3^*	5.0^*	3.1^*
SXYL_01914	murE	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate–L-lysine ligase	6.2	5.2	3.6
SXYL_02166	uppP	Undecaprenyl-diphosphatase	2.5	2.3	2.2
SXYL_01624	uppS	Isoprenyl transferase	6.1	3.0	2.5
SXYL_01707	pbp1	Penicillin-binding protein 1	4.3	2.7	2.0
SXYL_01304	pbp3	Penicillin-binding protein 3	2.6	3.3	2.7
Teichoic acid synthesis
SXYL_02208	tagD	Glycerol-3-phosphate cytidylyltransferase	0.2	0.2	0.3
SXYL_01022		Teichoic acid translocation permease protein	6.4	5.9	4.6
SXYL_01987-90	dltDCBA	Teichoic acid biosynthesis	7.6^*	4.7^*	2.6^*
Membrane proteins
SXYL_01650	ftsY	Signal recognition particle receptor FtsY	4.2	4.8	3.0
SXYL_00842	yidC	Membrane protein insertase YidC	2.7	2.0	2.1
SXYL_02419	ftsH	ATP-dependent zinc metalloprotease FtsH	11.7	12.0	8.2
Lipid/Phospholipid synthesis
SXYL_01167-68	accDA	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta and alpha	3.6^*	3.7^*	3.0^*
SXYL_01326-27	accBC	Acetyl-CoA carboxylase, biotin carboxyl carrier protein and carboxylase subunit	5.6^*	3.2^*	2.4^*
SXYL_01655-54	fabDG	Malonyl CoA-acyl carrier protein transacylase, 3-oxoacyl-[acyl-carrier protein] reductase	8.9^*	8.6^*	5.1^*
SXYL_01944-43	fabHF	3-oxoacyl-[acyl-carrier-protein] synthase 3 and 2	2.7^*	2.6^*	2.1
SXYL_01921	fabI	Enoyl-[acyl-carrier-protein] reductase [NADPH]	2.5	2.3
SXYL_01656	plsX	Phosphate acyltransferase	13.3	9.8	6.6
SXYL_01657	fapR	Transcription factor FapR	8.0	5.1	3.2
Regulator/Sensor
SXYL_01427-28	arlSR	Signal transduction histidine-protein kinase ArlS, Regulator ArlR	2.6^*	3.9^*	2.8^*
SXYL_00951	vraS	Sensor protein VraS	3.8	4.6	2.7
Lysis
SXYL_00365-67	cidABC	Holin-like proteins CidA and CidB, Pyruvate oxidase	23.4^*	10.4^*	9.1^*
SXYL_00494	lrgA	Antiholin-like protein LrgA		2.6
SXYL_01730-82		Phage proteins		13,9^*	14.1^*
SXYL_01785		Phage repressor-like protein	0.3	0.4	0.5
SXYL_01783		Phage antirepressor protein	2.8	24.6	22.2
CARBOHYDRATE METABOLISM
SXYL_00699	glcU	Glucose uptake protein	10.2	7.8	5.4
Pentose phosphate pathway
SXYL_00698	gdh	Glucose 1-dehydrogenase	3.0	3.2	2.8
SXYL_00361		Gluconolactonase	3.9	3.4	2.5
SXYL_00438-40	gntRKP	Gluconate Repressor, Kinase, Permease	19.8^*	38.6^*	16.1^*
SXYL_00568	rpi	Ribose-5-phosphate isomerase		2.5	3.0
EMBDEN-meyerhof-parnas pathway
SXYL_01308	glkA	Glucokinase	2.8	2.9
SXYL_02069-67	pgk, tpiA, gpmI	Phosphoglycerate kinase, Triosephosphate isomerase, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase	6.5^*	4.5^*	3.1^*
Pyruvate metabolism
SXYL_00250		L-lactate permease		2.5	2.6
SXYL_00170	lqo	L-lactate-quinone oxidoreductase	2.5
SXYL_00276	ldhB	L-lactate dehydrogenase	0.2	0.3	0.4
SXYL_01023-24	pflAB	Formate acetyltransferase	2.2^*	2.3^*	2.1^*
SXYL_01839-42	pdhABCD	Pyruvate dehydrogenase complex	3.7^*	3.4^*	2.9^*
SXYL_00194	lplA	Lipoate-protein ligase A	6.4	11.3	6.1
SXYL_02616		Acetate-CoA ligase	3.5	4.3	3.6
TCA CYCLE AND RESPIRATORY CHAIN
SXYL_01793-95	sdhABC	Succinate dehydrogenase	3.0^*	4.4^*	3.5^*
SXYL_01636-37	sucCD	Succinyl-CoA synthase		2.5^*	2.2^*
SXYL_00579	mqo	Malate:quinone oxidoreductase	5.0	6.3	4.7
SXYL_00824-31	atpBEFHAGDC	F0F1-type ATP synthase	8.7^*	5.5^*	4.0^*
SXYL_00823	atpI	Putative ATP synthase protein I	7.3	3.7	2.6
SXYL_00539-42	narGHIJ	Respiratory nitrate reductase	4.2^*	4.4^*	3.1^*
SXYL_00534-36	nirBD, sirB	Nitrite reductase	6.3^*	3.6^*	3.3^*
SXYL_00547	narT	Nitrate transporter NarT	2.3
SXYL_00530		Formate/nitrite transporter	2.9	2.2	2.4
Regulators
SXYL_00544	nreB	Oxygen sensor histidine kinase NreB	2.1
SXYL_01366	srrB	Sensor histidine kinase SrrB	2.7	2.1
SXYL_00883	rex	Redox-sensing transcriptional repressor Rex	0.4	0.4	0.4
COFACTOR, VITAMIN SYNTHESIS
Molybdenum
SXYL_00675-77	modABC	Molybdate ABC transporter	5.5^*	5.0^*	3.7^*
SXYL_00682-87	moeA, mobAB, moaAE	Molybdenum biosynthesis	3.0^*	3.1^*	2.9^*
SXYL_00679	moeB	Molybdopterin biosynthesis protein MoeB	2.1	1.8	1.7
Heme
SXYL_01196-99	hemCDBL1	Heme biosynthesis	3.3^*	4.0^*	3.2^*
SXYL_01274	hemN	Oxygen-independent coproporphyrinogen oxidase III	6.6	5.0	3.2
SXYL_00972	hemL2	Glutamate-1-semialdehyde 2,1-aminomutase 2	3.1	3.3	2.5
SXYL_01040-41	hemHG	Heme biosynthesis	4.2^*	4.9^*	5.6^*
SXYL_01819	ctaB	Protoheme IX farnesyltransferase	2.8		2.5
SXYL_00751-53	htsABC	heme transport system	2.9^*	2.8^*	2.4^*
SXYL_00755	isdG	Heme-degrading monooxygenase	0.2	0.2	0.3
SXYL_00749	sfaB	Siderophore biosynthesis protein, IucA/IucC family	0.1	0.2	0.2
SXYL_00944	ftnA	Ferritin	0.2	0.3	0.4
Menaquinone
SXYL_01079-80	menEC	Menaquinone biosynthesis	2.3	2.8^*	2.1
SXYL_01891-92	menHD	Menaquinone biosynthesis	3.2^*	5.2^*	4.2^*
Riboflavin
SXYL_01097-100	ribDEBAH	Riboflavin biosynthesis protein	0.2^*	0.2^*	0.3^*
Folate
SXYL_02414-16	folKBP	Folate biosynthesis	5.1^*	5.1^*	3.4^*
SXYL_01203	folC	Tetrahydrofolate synthase	3.6	2.2
SXYL_01872	folD	Bifunctional protein FolD	7.3	4.6	3.3
SXYL_01261	aroE	Shikimate dehydrogenase	4.4	4.3	2.7
PEPTIDE AND AMINO ACID METABOLISM
Transport
SXYL_00300-02		Oligopeptide ABC transporter	2.9^*	2.9^*	2.3^*
SXYL_01184	lysP	Lysine-specific permease	7.1	6.9	4.5
SXYL_01528		Sodium:alanine symporter	5.11
SXYL_01919		Sodium:alanine symporter	0.45		2.78
SXYL_02518	gltT	Proton/sodium-glutamate symporter	2.3
Peptidase
SXYL_01247-48		U32 family peptidases	5.8^*	4.5^*	3.2^*
SXYL_00957	ampS	Leucyl aminopeptidase	3.4	2.7	2.2
SXYL_00948	map	Methionine aminopeptidase	3.0	3.0	2.0
Valine, leucine, isoleucine
SXYL_00867-75	ilvA, leuDCBA, ilvCNBD1	Valine, leucine, isoleucine biosynthesis	0.3^*	0.1^*	0.1^*
SXYL_02469	ilvD2	Dihydroxy-acid dehydratase	0.2	0.1	0.1
SXYL_01337-40	lpdA, bkdA1A2	alpha-keto acid dehydrogenase complex	4.9^*	3.7^*	2.8^*
Tryptophan, phenylalanine, tyrosine
SXYL_01383-85	aroABC	Aromatic acid biosynthesis	0.3^*	0.3^*	0.2^*
SXYL_02022	aroD	3-dehydroquinate dehydratase	0.2	0.3	0.3
SXYL_01497	trpA	Tryptophan synthase alpha chain	0.4	0.4	0.5
SXYL_01128		DAHP synthetase-chorismate mutase	0.1	0.0	0.1
Histidine
SXYL_00460-68	hisZGDCBHAFI	Histidine biosynthesis	0.1^*	0.1^*	0.1^*
Cysteine, methionine
SXYL_02644	metE	5-methyltetrahydropteroyltriglutamate–homocysteine methyltransferase	0.1	0.1	0.2
SXYL_00372		D-cysteine desulfhydrase	0.3	0.4	0.4
Arginine
SXYL_00238-41	rocD1, argCJB	Arginine biosynthesis	0.3^*	0.2^*	0.3^*
SXYL_00252	arcB	Ornithine carbamoyltransferase	0.3	0.3	0.4
SXYL_01961-62	argGH	Arginine biosynthesis	0.3^*	0.2^*	0.2^*
SXYL_01355	proC	Pyrroline-5-carboxylate reductase	0.3	0.3	0.3
Aspartate
SXYL_01002	panD	Aspartate 1-decarboxylase	0.4	0.2	0.2
SXYL_01558		Aspartokinase	0.4	0.3	0.4
SXYL_01373	asnA	L-asparaginase	2.6	2.8	2.4
Glutamate, glutamine
SXYL_01964	gluD1	Glutamate dehydrogenase		2.3
SXYL_02326	gluD2	Glutamate dehydrogenase	3.5
SXYL_02459-61	gltBCD	Glutamate synthase	2.6^*
SXYL_00105		Membrane protein, EutH superfamily	20.3	29.3	12.9
SXYL_00106		Short-chain dehydrogenase	41.3	29.4	13.9
SXYL_00107	glnA2	Glutamine synthetase	41.7	29.2	15.7
SXYL_00108		Aldehyde dehydrogenase	41.3	29.5	15.4
RESPONSE TO OSMOTIC STRESS
SXYL_01536	mscL	Large-conductance mechanosensitive channel	0.3	0.2	0.3
Synthesis and accumulation of osmoprotectant
SXYL_00488-91	opuCABCD	Glycine betaine/carnitine/choline ABC transporter	24.8^*	6.1^*	4.3^*
SXYL_00486	lcdH	L-carnitine dehydrogenase	22.8	5.0	3.3
SXYL_00223-26	cudTCA, betA	Glycine betaine/carnitine/choline ABC transporter	7.9^*	3.7^*	3.4^*
SXYL_01171	aapA	D-serine/D-alanine/glycine transporter	2.6	2.8	2.3
SXYL_00317		D-serine/D-alanine/glycine transporter	4.9	6.1	4.4
SXYL_02528-29	sdaAA1AB1	L-serine dehydratase, alpha subunit and beta subunit	3.8^*	5.0^*	4.0^*
SXYL_00820	glyA	Serine hydroxymethyltransferase	10.7	7.4	5.4
SXYL_01084	metK	S-adenosylmethionine synthetase	6.8	8.3	4.8
SXYL_02526		Sodium:dicarboxylate symporter	11.2	3.7
Na⁺/H⁺ antiporter
SXYL_01970-76	mnhA1B1C1D1E1F1G1	Na(+)/H(+) antiporter	6.1^*	6.3^*	3.4^*
SXYL_02220-26	mnhG2F2E2D2C2B2A2	Na(+)/H(+) antiporter	4.8^*	4.6^*	2.8^*
Regulator
SXYL_00859	rsbU	Serine phosphatase RsbU, regulator of sigma subunit	4.2	2.9	2.8
SXYL_00860	rsbV	Anti-sigma-B factor antagonist	0.3	0.2	0.2
SXYL_00861	rsbW	Serine-protein kinase RsbW	0.2	0.2	0.2
STRESS RESPONSE AND PIGMENTATION
SXYL_01551	katB	Catalase B	0.2	0.3	0.4
SXYL_02533	katC	Catalase C	0.2	0.2	0.2
SXYL_01572	bsaA	Glutathione peroxidase	0.2	0.4	0.4
SXYL_00374		Thioredoxin	0.1	0.2	0.2
SXYL_00051-54	crtPQMN	pigment biosynthesis	7.8^*	6.3^*	3.9^*
SXYL_00358	mvaS	3-hydroxy-3-methylglutaryl CoA synthase	2.2
SXYL_00359-60	mvaCA	Acetyl-CoA acetyltransferase, Hydroxymethylglutaryl-CoA reductase	2.4^*	2.2^*
SXYL_02258-56	mvaK1DK2	Mevalonate kinase, Diphosphomevalonate decarboxylase, Phosphomevalonate kinase	5.0^*	4.4^*	2.9^*
SXYL_00599	fni	Isopentenyl-diphosphate delta-isomerase	2.2	3.2	2.5
SXYL_01332	ispA	Geranyltranstransferase	4.6	3.8	2.5
SXYL_00309		Universal stress protein	0.1	0.2	0.2
SXYL_01162		Universal stress protein	0.2	0.2	0.2
SXYL_00196		General stress protein	0.0	0.0	0.0

Means of the expression of the clustered genes differentially expressed.