Table 4.

A selection of the stress response-encoding genes, the defined sub-system, together with the gene name, length of the ORF and correspondoing function, identified in C. sakazakii SP291.

Category	Sub-system	Gene	Size (bp)	Function
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	betB	1472	Betaine aldehyde dehydrogenase
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	betA	1679	Choline dehydrogenase
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	betI	608	HTH-type transcriptional regulator BetI
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	betT	2030	High-affinity choline uptake protein BetT
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	opuCA	1145	Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	opuCB	647	Glycine betaine/carnitine/choline transport ATP-binding protein OpuCB
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	opuCC	905	Glycine betaine/carnitine/choline transport ATP-binding protein OpuCC
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	opuCD	713	Glycine betaine/carnitine/choline transport ATP-binding protein OpuCD
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	proP	1506	L-Proline/Glycine betaine transporter ProP
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	proV	1202	L-Proline/Glycine betaine ABC transport system permease protein ProV
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	proW	1070	L-proline glycine betaine ABC transport system permease protein ProW
Osmotic stress	Choline and betaine uptake and betaine biosynthesis	proX	995	L-proline glycine betaine binding ABC transporter protein ProX
Osmotic stress	Osmoprotectant ABC transporter YehZYXW of enterobacteriales	yehX	941	Osmoprotectant ABC transporter ATP-binding subunit YehX
Osmotic stress	Osmoprotectant ABC transporter YehZYXW of enterobacteriales	yehZ	908	Osmoprotectant ABC transporter binding protein YehZ
Osmotic stress	Osmoprotectant ABC transporter YehZYXW of enterobacteriales	yehW	731	Osmoprotectant ABC transporter inner membrane protein YehW
Osmotic stress	Osmoprotectant ABC transporter YehZYXW of enterobacteriales	yehY	1133	Osmoprotectant ABC transporter permease protein YehY
Osmotic stress	Osmoregulation	aqpZ	695	Aquaporin Z
Osmotic stress	Osmoregulation	glpF	848	Glycerol uptake facilitator protein
Osmotic stress	Osmoregulation	osmY	614	Osmotically inducible protein OsmY
Osmotic stress	Osmoregulation	ompA	1076	Outer membrane protein A precursor
Osmotic stress	Osmoregulation	yiaD	662	Inner membrane lipoprotein yiaD
Osmotic stress	Osmotic stress cluster	yciM	1169	Heat shock (predicted periplasmic) protein YciM, precursor
Osmotic stress	Osmotic stress cluster	osmB	215	Osmotically inducible lipoprotein B precursor
Osmotic stress	Osmotic stress cluster	pgpB	764	Phosphatidylglycerophosphatase B
Osmotic stress	Osmotic stress cluster	yciT	800	Transcriptional regulatory protein YciT
Osmotic stress	Synthesis of osmoregulated periplasmic glucans	mdoH	2528	Glucans biosynthesis glucosyltransferase H
Osmotic stress	Synthesis of osmoregulated periplasmic glucans	mdoC	1157	Glucans biosynthesis protein C
Osmotic stress	Synthesis of osmoregulated periplasmic glucans	mdoD	1715	Glucans biosynthesis protein D precursor
Osmotic stress	Synthesis of osmoregulated periplasmic glucans	mdoG	1553	Glucans biosynthesis protein G precursor
Osmotic stress	Synthesis of osmoregulated periplasmic glucans	opgC	1220	OpgC protein
Osmotic stress	Synthesis of osmoregulated periplasmic glucans	mdoB	2294	Phosphoglycerol transferase I
Cold shock	Cold shock, CspA family of proteins	cspA	212	Cold shock protein CspA
Cold shock	Cold shock, CspA family of proteins	cspC	209	Cold shock protein CspC
Cold shock	Cold shock, CspA family of proteins	cspD	230	Cold shock protein CspD
Cold shock	Cold shock, CspA family of proteins	cspE	209	Cold shock protein CspE
Cold shock	Cold shock, CspA family of proteins	cspG	212	Cold shock protein CspG
Heat shock	Heat shock dnaK gene cluster extended	dnaJ	1139	Chaperone protein DnaJ
Heat shock	Heat shock dnaK gene cluster extended	dnaK	1700	Chaperone protein DnaK
Heat shock	Heat shock dnaK gene cluster extended	yggX	275	FIG001341:,Probable Fe(2+)-trafficking protein YggX
Heat shock	Heat shock dnaK gene cluster extended	gshB	947	Glutathione synthetase
Heat shock	Heat shock dnaK gene cluster extended	grpE	602	Heat shock protein GrpE
Heat shock	Heat shock dnaK gene cluster extended	rdgB	593	Nucleoside 5-triphosphatase RdgB (dHAPTP, dITP, XTP-specific)
Heat shock	Heat shock dnaK gene cluster extended	rpoH	857	RNA polymerase sigma factor RpoH
Heat shock	Heat shock dnaK gene cluster extended	hemN2	1136	Radical SAM family enzyme, similar to coproporphyrinogen III oxidase, oxygen-independent, clustered with nucleoside-triphosphatase RdgB
Heat shock	Heat shock dnaK gene cluster extended	rph	635	Ribonuclease PH
Heat shock	Heat shock dnaK gene cluster extended	rsmE	731	16S rRNA methyltransferase RsmE
Heat shock	Heat shock dnaK gene cluster extended	prmA	881	Ribosomal protein L11 methyltransferase
Heat shock	Heat shock dnaK gene cluster extended	hslR	401	Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog)
Heat shock	Heat shock dnaK gene cluster extended	lepA	1799	Translation elongation factor LepA
Heat shock	Heat shock dnaK gene cluster extended	yraL	860	rRNA small subunit methyltransferase I
Heat shock	Heat shock dnaK gene cluster extended	smpB	482	tmRNA-binding protein SmpB
Dessication stress	O-antigen capsule important for environmental persistence	yihT	875	Aldolase YihT
Dessication stress	O-antigen capsule important for environmental persistence	yihS	1241	Aldose-ketose isomerase YihS
Dessication stress	O-antigen capsule important for environmental persistence	yihQ	2030	Alpha-glucosyltransferase YihQ
Dessication stress	O-antigen capsule important for environmental persistence	yihW	806	DeoR-type transcriptional regulator YihW
Dessication stress	O-antigen capsule important for environmental persistence	yihO	1430	Glucuronide transport protein YihO
Dessication stress	O-antigen capsule important for environmental persistence	yihP	1406	Glucuronide transport protein YihP, homologous to YihO
Dessication stress	O-antigen capsule important for environmental persistence	yshA	686	Outer membrane sugar transport protein YshA
Dessication stress	O-antigen capsule important for environmental persistence	yihU	899	Oxidoreductase YihU
Dessication stress	O-antigen capsule important for environmental persistence	yihV	899	Sugar kinase YihV
Dessication stress	O-antigen capsule important for environmental persistence	yihR	866	Sugar-1-epimerase YihR
Detoxification	D-tyrosyl-tRNA(Tyr) deacylase	dtd	437	D-tyrosyl-tRNA(Tyr) deacylase
Detoxification	Glutathione-dependent pathway of formaldehyde detoxification	frmA	1118	S-(hydroxymethyl)glutathione dehydrogenase
Detoxification	Glutathione-dependent pathway of formaldehyde detoxification	yieG	830	S-formylglutathione hydrolase YeiG
Detoxification	Tellurite resistance: chromosomal determinants	ydsK	980	Uncharacterized acetyltransferase ydcK
Detoxification	Tellurite resistance: chromosomal determinants	tehB	593	Tellurite resistance protein TehB
Detoxification	Tellurite resistance: chromosomal determinants	ydcL	668	Uncharacterized lipoprotein ydcL
Detoxification	Uptake of selenate and selenite	dedA	659	DedA protein
Detoxification	Uptake of selenate and selenite	cysA	1094	Sulfate and thiosulfate import ATP-binding protein CysA
Detoxification	Uptake of selenate and selenite	tsgA	1187	TsgA protein homolog
Oxidative stress	Glutaredoxins	yebA	1331	Uncharacterized metalloprotease yebA
Oxidative stress	Glutaredoxins	yibP	1259	Uncharacterized protein yibP
Oxidative stress	Glutaredoxins	hmp	1190	Flavohemoprotein (Hemoglobin-like protein) (Flavohemoglobin) (Nitric oxide dioxygenase)
Oxidative stress	Glutaredoxins	grxB	647	Glutaredoxin 2
Oxidative stress	Glutaredoxins	grxC	251	Glutaredoxin 3 (Grx3)
Oxidative stress	Glutaredoxins	nrdH	245	Glutaredoxin-like protein NrdH, required for reduction of Ribonucleotide reductase class Ib
Oxidative stress	Glutaredoxins	grlA	347	Probable monothiol glutaredoxin GrlA
Oxidative stress	Glutathione: biosynthesis and gamma-glutamyl cycle	ggt	1766	Gamma-glutamyltranspeptidase
Oxidative stress	Glutathione: biosynthesis and gamma-glutamyl cycle	gshA	1556	Glutamate-cysteine ligase
Oxidative stress	Glutathione: biosynthesis and gamma-glutamyl cycle	gshB	947	Glutathione synthetase
Oxidative stress	Glutathione: non-redox reactions	rnhA	716	FIG005121: SAM-dependent methyltransferase
Oxidative stress	Glutathione: non-redox reactions	gst1	668	Glutathione S-transferase
Oxidative stress	Glutathione: non-redox reactions	yghU	866	Uncharacterized Glutathione S-transferase like protein yghU
Oxidative stress	Glutathione: non-redox reactions	gst	608	Glutathione S-transferase
Oxidative stress	Glutathione: non-redox reactions	yqjG	986	Uncharacterized protein yqjG
Oxidative stress	Glutathione: non-redox reactions	gloB	755	Hydroxyacylglutathione hydrolase
Oxidative stress	Glutathione: non-redox reactions	gloA	407	Lactoylglutathione lyase
Oxidative stress	Glutathione: non-redox reactions	yfcF	644	Probable glutathione S-transferase, YfcF homolog
Oxidative stress	Glutathione: non-redox reactions	yfcG	626	Probable glutathione S-transferase, YfcG homolog
Oxidative stress	Glutathione: non-redox reactions	yibF	608	Uncharacterized GST-like protein yibF
Oxidative stress	Glutathione: non-redox reactions	yliJ	626	Uncharacterized glutathione S-transferase-like protein
Oxidative stress	Glutathione: redox cycle	grxB	635	Glutaredoxin 2
Oxidative stress	Glutathione: redox cycle	grxC	251	Glutaredoxin 3 (Grx3)
Oxidative stress	Glutathione: redox cycle	nrdH	245	Glutaredoxin-like protein NrdH, required for reduction of Ribonucleotide reductase class Ib
Oxidative stress	Glutathione: redox cycle	btuE	551	Glutathione peroxidase
Oxidative stress	Glutathione: redox cycle	lpd	1427	Glutathione reductase
Oxidative stress	Glutathione: redox cycle	gor	1352	Glutathione reductase
Oxidative stress	Glutathionylspermidine and Trypanothione	yjfC	1187	Uncharacterized protein yjfC
Oxidative stress	Glutathionylspermidine and Trypanothione	ygiC	1160	Uncharacterized protein ygiC
Oxidative stress	NADPH:quinone oxidoreductase 2	ytfG	854	Uncharacterized oxidoreductase ytfG
Oxidative stress	NADPH:quinone oxidoreductase 2	qorR	380	Redox-sensing transcriptional regulator QorR
Oxidative stress	Oxidative stress	katG	2180	Catalase/peroxidase HPI
Oxidative stress	Oxidative stress	katE	2255	Hydroperoxidase II
Oxidative stress	Oxidative stress	fur	452	Ferric uptake regulation protein FUR
Oxidative stress	Oxidative stress	dps	503	DNA protection during starvation protein
Oxidative stress	Oxidative stress	fnr	752	Fumarate and nitrate reduction regulatory protein
Oxidative stress	Oxidative stress	oxyR	917	DNA-binding transcriptional regulator OxyR
Oxidative stress	Oxidative stress	dps	503	DNA protection during starvation protein
Oxidative stress	Oxidative stress	sodA	626	Manganese superoxide dismutase
Oxidative stress	Oxidative stress	nsrR	353	Nitrite-sensitive transcriptional repressor NsrR
Oxidative stress	Oxidative stress	dpS	503	Non-specific DNA-binding protein Dps
Oxidative stress	Oxidative stress	osmC	428	Organic hydroperoxide resistance
Oxidative stress	Oxidative stress	ohrR	548	Organic hydroperoxide resistance transcriptional regulator
Oxidative stress	Oxidative stress	yebS	1283	Inner membrane protein yebS
Oxidative stress	Oxidative stress	pqiA	1284	Paraquat-inducible protein A
Oxidative stress	Oxidative stress	yebT	2633	Uncharacterized protein yebT
Oxidative stress	Oxidative stress	ymbA	563	Uncharacterized lipoprotein ymbA
Oxidative stress	Oxidative stress	pqiB	1640	Paraquat-inducible protein B
Oxidative stress	Oxidative stress	katG	2180	Catalase/peroxidase HPI
Oxidative stress	Oxidative stress	soxR	458	Redox-sensitive transcriptional activator SoxR
Oxidative stress	Oxidative stress	soxS	323	Regulatory protein SoxS
Oxidative stress	Oxidative stress	sodC	518	Superoxide dismutase [Cu-Zn] precursor
Oxidative stress	Oxidative stress	zur	515	Zinc uptake regulation protein Zur
Oxidative stress	Protection from reactive oxygen species	katG	2180	Catalase/peroxidase HPI
Oxidative stress	Protection from reactive oxygen species	katE	2255	Hydroperoxidase II
Oxidative stress	Protection from reactive oxygen species	sodA	626	Manganese superoxide dismutase
Oxidative stress	Protection from reactive oxygen species	sodC	518	Superoxide dismutase [Cu-Zn] precursor
Oxidative stress	Redox-dependent regulation of nucleus processes	gapA1	995	NAD-dependent glyceraldehyde-3-phosphate dehydrogenase
Oxidative stress	Redox-dependent regulation of nucleus processes	gapA2	996	NAD-dependent glyceraldehyde-3-phosphate dehydrogenase
Oxidative stress	Redox-dependent regulation of nucleus processes	npdA	824	NAD-dependent protein deacetylase of SIR2 family
Oxidative stress	Redox-dependent regulation of nucleus processes	pncA	641	Nicotinamidase
Oxidative stress	Redox-dependent regulation of nucleus processes	pncB	1202	Nicotinate phosphoribosyltransferase
Periplasmic stress	Periplasmic stress response	htrA	1427	HtrA protease/chaperone protein
Periplasmic Stress	Periplasmic stress response	skp	494	Outer membrane protein H precursor
Periplasmic Stress	Periplasmic stress response	degQ	1367	Outer membrane stress sensor protease DegQ, serine protease
Periplasmic Stress	Periplasmic stress response	degS	1067	Outer membrane stress sensor protease DegS
Periplasmic Stress	Periplasmic stress response	rseA	650	Sigma factor RpoE negative regulatory protein RseA
Periplasmic Stress	Periplasmic stress response	rseB	854	Sigma factor RpoE negative regulatory protein RseB precursor
Periplasmic Stress	Periplasmic Stress response	surA	1286	Survival protein SurA precursor (Peptidyl-prolyl cis-trans isomerase SurA)
No subcategory	Bacterial hemoglobins	hmp	1190	Flavohemoprotein (Hemoglobin-like protein) (Flavohemoglobin) (Nitric oxide dioxygenase)
No subcategory	Carbon starvation		2105	Carbon starvation protein A
No subcategory	Carbon starvation	cstA	2153	Carbon starvation protein A paralog
No subcategory	Carbon starvation	csrA	185	Carbon storage regulator
No subcategory	Carbon starvation		584	Starvation lipoprotein Slp paralog
No subcategory	Carbon starvation	rspA	1316	Starvation sensing protein RspA
No subcategory	Carbon starvation	sspA	641	Stringent starvation protein A
No subcategory	Carbon starvation	sspB	491	Stringent starvation protein B
No subcategory	Commensurate regulon activation	marA	374	Multiple antibiotic resistance protein MarA
No subcategory	Commensurate regulon activation	gpmB	869	Probable phosphoglycerate mutase gpmB
No subcategory	Commensurate regulon activation	soxS	324	Regulatory protein SoxS
No subcategory	Commensurate regulon activation	ramA	344	Transcriptional activator RamA
No subcategory	Flavohaemoglobin	hmp	1190	Flavohemoprotein (Hemoglobin-like protein) (Flavohemoglobin) (Nitric oxide dioxygenase)
No subcategory	Hfl operon	hflX	1280	GTP-binding protein HflX
No subcategory	Hfl operon	hflC	1004	HflC protein
No subcategory	Hfl operon	hflK	1244	HflK protein
No subcategory	Hfl operon	yjeT	197	Putative inner membrane protein YjeT (clustered with HflC)
No subcategory	Hfl operon	hfq	308	RNA-binding protein Hfq
No subcategory	Phage shock protein (psp) operon	pspA	671	Phage shock protein A
No subcategory	Phage shock protein (psp) operon	pspB	224	Phage shock protein B
No subcategory	Phage shock protein (psp) operon	pspC	356	Phage shock protein C
No subcategory	Phage shock protein (psp) operon	pspD	242	Phage shock protein D
No subcategory	Phage shock protein (psp) operon	pspF	1001	Psp operon transcriptional activator
No subcategory	Sugar-phosphate stress regulation	sgrR	1664	SgrR, sugar-phosphate stress, transcriptional activator of SgrS small RNA
No subcategory	Universal stress protein family	uspA	437	Universal stress protein A
No subcategory	Universal stress protein family	uspB	335	Universal stress protein B
No subcategory	Universal stress protein family	uspC	422	Universal stress protein C
No subcategory	Universal stress protein family	uspE	956	Universal stress protein E
No subcategory	Universal stress protein family	uspG	428	Universal stress protein G