TABLE 4.

Proteins identified as being expressed in a σ^B-dependent manner in stationary-phase extracts from BHIS, analyzed by the iTRAQ method

Protein	Homology (% identity/% similarity)a	Microorganism with homologous proteinb	Change (fold)b	P value
Lmo2391c	YhfK (42/61)	Bacillus subtilis	−14.3	1.59 × 10−7
Lmo0265	Succinyldiaminopimelate desuccinylase, DapE (100/100)	Listeria monocytogenes	−14.3	3.36 × 10−4
Lmo0539c	Tagatose-1,6-diphosphate aldolase (55/76)	Staphylococcus aureus	−6.3	1.59 × 10−7
Lmo2695	Dihydroxyacetone kinase (60/78)	Lactococcus lactis	−4.0	1.59 × 10−7
OpuCC	Glycine betaine/carnitine/choline ABC transporter (100/100)	Listeria monocytogenes	−3.8	9.80 × 10−4
Lmo2205	Phosphoglycerate mutase (57/72)	Bacillus anthracis	−3.7	1.59 × 10−7
Lmo0796c	YceI (44/61)	Escherichia coli	−3.3	1.59 × 10−7
Lmo2696c	Dihydroxyacetone kinase (50/68)	Lactococcus lactis	−3.2	1.59 × 10−7
Lmo2697	PTS-dependent dihydroxyacetone kinase phosphotransferase subunit (46/72)	Lactococcus lactis	−3.1	3.59 × 10−6
Lmo1601	YtxH (49/62)	Bacillus sp. NRRL	−2.9	1.59 × 10−7
Lmo1602	YtxG (40/66)	Bacillus licheniformis	−2.5	1.59 × 10−7
Lmo0956	N-Acetylglucosamine-6-phosphate deacetylase (61/77)	Lactobacillus salivarius	−1.9	6.59 × 10−6
Lmo0398	PTS fructose-specific IIABC component (37/63)	Mycoplasma hyopneumoniae	−1.6	2.19 × 10−5
Lmo0292	Heat shock protein HtrA serine protease (100/100)	Listeria monocytogenes	−1.6	1.88 × 10−2
Lmo2824	d-3-Phosphoglycerate dehydrogenase (56/76)	Bacillus thuringiensis	1.5	1.59 × 10−7
PyrF	Orotidine 5′-phosphate decarboxylase (63/75)	Bacillus subtilis	1.5	1.38 × 10−3
ProS	Prolyl-tRNA synthetase (100/100)	Listeria monocytogenes	1.5	7.42 × 10−6
TcsA	CD4+ T-cell-stimulating antigen, lipoprotein (100/100)	Listeria monocytogenes	1.6	1.59 × 10−7
Lmo0344	Dehydrogenase/reductase (55/75)	Pseudomonas syringae	1.6	4.98 × 10−7
Lmo0443	Transcription regulator LytR (35/56)	Bacillus subtilis	1.6	6.50 × 10−6
DaaA	d-Amino acid aminotransferase (100/100)	Listeria monocytogenes	1.6	5.44 × 10−4
Lmo0342	Transketolase (59/74)	Bacillus thuringiensis	1.6	4.08 × 10−3
DeoD	Purine nucleoside phosphorylase (100/100)	Listeria monocytogenes	1.7	1.56 × 10−4
Lmo1699	Methyl-accepting chemotaxis protein (41/59)	Bacillus sp. NRRL	1.7	2.84 × 10−3
Lmo1681	Cobalamin-independent methionine synthase, MetE (53/71)	Bacillus subtilis	1.7	2.14 × 10−2
DltD	DltD protein for d-alanine esterification of lipoteichoic acid and wall teichoic acid (100/100)	Listeria monocytogenes	1.7	4.50 × 10−4
Lmo0560	NADP-specific glutamate dehydrogenase (70/83)	Bacillus clausii	1.8	1.59 × 10−7
Lmo1057	l-Lactate dehydrogenase (32/54)	Bacillus licheniformis	1.8	1.23 × 10−5
Lmo0521	6-Phospho-beta-glucosidase (67/80)	Bacillus subtilis	1.8	6.53 × 10−7
Lmo2363	Glutamate decarboxylase, GadB (100/100)	Listeria monocytogenes	1.8	1.59 × 10−7
Lmo1604	2-Cys peroxiredoxin (70/87)	Bacillus halodurans	1.8	2.21 × 10−2
Lmo2258	Ribulose-phosphate 3-epimerase (90/95)	Listeria welshimeri	1.9	2.43 × 10−4
Lmo0536	6-Phospho-beta-glucosidase (60/73)	Bacillus subtilis	1.9	1.20 × 10−2
Lmo2362	Amino acid antiporter, GadC (100/100)	Listeria monocytogenes	2.3	3.40 × 10−2
Lmo1867	Pyruvate phosphate dikinase (60/75)	Clostridium difficile	3.1	6.10 × 10−3

^aThe identity and similarity values were obtained by performing a protein-protein BLAST search on the NCBI website (http://www.ncbi.nlm.nih.gov/BLAST/). It should be emphasized that most of the functions indicated are putative.

^bThe changes indicate the expression ratio for the ΔsigB mutant and the wild type (ΔsigB/wild type), expressed as a negative reciprocal for proteins that were present at reduced levels in the ΔsigB strain.

^cThe protein was also determined to be expressed in a σ^B-dependent manner using the 2-DGE technique.