TABLE 1.

Proteins/genes predicted to play a role in the catabolism of XOS in B. animalis subsp. lactis BB-12^a

IDb	Description	Predicted function	Fold change upregulation on XOSc			Additional informationd
			DNA microarrays	qPCR	2D-DIGE
501	Xylose isomerase	Isomerization of d-xylose to d-xylulose	32	19+++	13	EC 5.3.1.5 COG2115, XylA (2 × 10−156)
405	β-Xylosidase	Cleavage of nonreducing end of β-1,4- xylo-oligosaccharides	6.1	3.0++	1.8	EC 3.2.1.37/EC 3.2.1.55 GH 43 (3 × 10−36); COG3507, XynB, β-xylosidase (4 × 10−34)
92	β-Xylosidase	Cleavage of nonreducing end of β-1,4- xylo-oligosaccharides	31	10.3+++	ND	EC 3.2.1.37/EC 3.2.1.55 GH 43 (1 × 10−84); COG3507, XynB, β-xylosidase (2 × 10−152)
432	Transcriptional repressor	Regulation of the transcription of the XOS gene cluster	2.1	1.1	ND	cd06267, PBP1_LacI_sugar_binding_like (8 × 10−66); cd01543, PBP1_XylR, ligand binding domain of DNA transcription repressor specific for xylose (1 × 10−15)
212	Sugar-binding protein	Binding of XOS at the cell surface	29	21+++	6.2	COG1653, UgpB, ABC-type sugar transport system periplasmic component (1 × 10−35); COG2182, MalE, maltose binding periplasmic proteins/domains (2 × 10−17)
257	Transporter	ABC-type permease, creating the pore in the membrane through which XOS are imported	25	28+++	ND	PRK10999, MalF, maltose transporter membrane protein (32%, 23%, 1 × 10−13); COG1175, UgpA, ABC-type sugar transport systems, permease components (7 × 10−58)
258	Transporter	ABC-type permease, creating the pore in the membrane through which XOS are imported	18	14+++	ND	COG3833, MalG, ABC-type maltose transport systems, permease component (32%, 25%, 7 × 10−37); TC 3.A.1.1.21e xylobiose porter BxlEFG(K) (31%, 22%, 2 × 10−34)
633	Endo-1,4-β-xylanase	Endohydrolysis of β-1,4-xylosidic linkages in XOS	5.9	2.1+	ND	EC 3.2.1.8 pfam04616, GH 43 (8 × 10−40); COG3507, XynB, β-xylosidase (3 × 10−46)
928	Endo-1,4-β-xylanase	Endohydrolysis of β-1,4-xylosidic linkages in XOS	2.2	2.5+	ND	EC 3.2.1.8 COG0657, Aes, esterase/lipase (6 × 10−16)
829	Xylulose kinase	Phosphorylation of xylulose to xylulose-5-P	4.8	3.4+++	ND	EC 2.7.1.17 TIGR01312, XylB, d-xylulose kinase (3 × 10−94)
1629	ABC transporter ATP- binding protein	Binding and hydrolysis of ATP to energize XOS transport via ABC-type transport systems	1.2	0.82	1.8	COG1129, MglA, ABC-type sugar transport systems, ATPase component (7 × 10−6)
1681	Sugar transport ATP-binding protein	Binding and hydrolysis of ATP to energize XOS transport via ABC-type transport systems	1.1	1.1	1.6	COG3839, MalK, ABC-type sugar transport systems, ATPase components (31%, 22%, 2 × 10−34)

^aFold-change upregulation values on XOS compared with glucose, as obtained using microarray (representing mean results of two analyses carried out using a dye swap), qPCR (mean of four values from four biological replicates, each run in duplicate), and 2D-DIGE analyses are listed. Information regarding function predictions is also given.

^bGene/protein number (the “BIF_” prefix was removed).

^c+, P < 0.05; ++, P < 0.01; +++, P < 0.001 (one-way ANOVA test). For complete data on the 2D-DIGE analysis see Table S2 in the supplemental material. ND, proteins not detected to be upregulated.

^dSequence-based similarities to conserved domains, as predicted using BLASTP (1) (percent amino acid identity, percent similarity, and expected values, respectively, are indicated in parentheses).

^eThe TC number corresponds to the Transporter Classification (TC) system and was predicted using the Transporter Classification Database (TCDB; http://www.tcdb.org/) (23).