TABLE 1.

Genes differentially expressed in B. subtilis 168 grown in the presence of methionine or sulfate as the sole sulfur source^a

Gene	Function/similarity	Transcriptome analysis		β-Galactosidase activity (U mg of protein−1)b
		Sulfate/methionine expression ratio	P value	Sulfate	Methionine	Sulfate/methionine expression ratio
Genes related to sulfur metabolism
cysJ	Sulfite reductase flavoprotein	1.52	5 × 10−3
cysI	Sulfite reductase hemoprotein	1.94	1 × 10−2
cysK	O-Acetylserine sulfhydrylase	0.66	2 × 10−3
mtnA	Methylthioadenosine nucleosidase	0.66	3 × 10−2
yrhA	Similar to O-acetylserine sulfhydrylase	0.44	2 × 10−3	28	106	0.26
yrhB	Similar to cystathionine γ-synthase	0.26	1 × 10−2	51	206	0.25
S-box family
metE	Probable cobalamin-independent methionine synthase	3.54	5 × 10−3	110	13	8.5
ykrW	Similar to ribulose bisphosphate carboxylase	1.95	3 × 10−2
ykrY	Similar to proteins of unknown function	4.84	1 × 10−2
ykrZ	Similar to proteins of unknown function	1.50	2 × 10−3	151	58	2.6
yoaD	Similar to phosphoglycerate dehydrogenase	2.00	2 × 10−3	125	8	15.6
yoaC	Similar to xylulokinase	1.80	1 × 10−2
yoaB	Similar to permease	1.80	4 × 10−3
yxjG	Similar to YxjH	1.50	3 × 10−3	115	27	4.3
yxjH	Similar to YxjG	2.37	1 × 10−2	146	32	4.6
Transporters and associated genes
ssuA	Aliphatic sulfonate ABC transporter (binding lipoprotein)	0.47	2 × 10−3
ssuC	Aliphatic sulfonate ABC transporter (permease)	0.52	5 × 10−3
ssuD	Aliphatic sulfonate monooxygenase	0.04	2 × 10−3
ygaN	Unknown	0.08	2 × 10−3
yhcL	Similar to sodium-glutamate symporter	0.29	2 × 10−3	22	223	0.10
ytmI	Similar to proteins of unknown function	0.55	8 × 10−3
ytmJ	Similar to amino acid ABC transporter (binding protein)	0.19	5 × 10−3
ytmK	Similar to amino acid ABC transporter (binding protein)	0.17	5 × 10−3
ytmL	Similar to amino acid ABC transporter (permease)	0.12	2 × 10−3
ytmM	Similar to amino acid ABC transporter (permease)	0.55	2 × 10−3
ytmN	Similar to amino acid ABC transporter (ATP-binding protein)	0.31	2 × 10−3
ytmO	Similar to proteins of unknown function	0.16	2 × 10−3
ytnI	Unknown	0.35	6 × 10−3
ribR	Riboflavin kinase	0.29	3 × 10−3
ytnL	Similar to aminohydrolase	0.51	3 × 10−3
ytnM	Unknown	0.16	2 × 10−3
yxeK	Similar to monooxygenase	0.40	3 × 10−2	55	292	0.19
yxeL	Similar to proteins of unknown function	0.66	1 × 10−2
yxeM	Similar to amino acid ABC transporter (binding protein)	0.50	2 × 10−2	33	353	0.09
yxeO	Similar to amino acid ABC transporter (ATP-binding protein)	0.66	1 × 10−2	15	150	0.10
yxeQ	Unknown	0.37	2 × 10−3	20	311	0.06
Regulator, ytlI	Similar to transcriptional regulator (LysR family)	0.66	4 × 10−2	12	216	0.05
Genes with other functions
accA	Acetyl-CoA carboxylase (alpha subunit)	2.15	2 × 10−2
appB	Oligopeptide ABC transporter (permease)	0.52	5 × 10−2
asnB	Asparagine synthetase	1.55	1 × 10−2
atpI	ATP synthase (subunit i)	1.80	4 × 10−3
folD	Probable methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase	1.90	1 × 10−2
glnR	Transcriptional repressor of the glutamine synthetase gene	1.90	3 × 10−2
hisB	Imidazoleglycerol-phosphate dehydratase	1.80	1 × 10−2
hisD	Histidinol dehydrogenase	1.76	8 × 10−3
hisI	Phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase	2.23	2 × 10−3
katA	Vegetative catalase 1	0.33	4 × 10−3	77	216	0.35
nadA	Probable quinolinate synthetase	1.95	3 × 10−3
nadC	Probable nicotinate-nucleotide pyrophosphorylase	1.40	2 × 10−3
nadB	l-Aspartate oxidase	1.69	3 × 10−3
nrgA	Ammonium transporter	1.70	1 × 10−2
pyrAA	Carbamoyl-phosphate synthetase (glutaminase subunit)	2.12	8 × 10−3
pyrE	Orotate phosphoribosyltransferase	2.93	6 × 10−3
yciA	Similar to proteins of unknown function	3.09	1 × 10−2
yciB	Similar to proteins of unknown function	1.80	6 × 10−3	3	0.8	3.70
yciC	Involved in low-affinity zinc transport system	2.44	1 × 10−2	161	55	3.00
ydbM	Similar to butyryl-CoA dehydrogenase	0.30	3 × 10−3	7	32	0.21

^aThe results obtained are representative of at least six hybridizations from five independent RNA extractions. The expression intensities of 3,830 genes were above the background level. Only genes with a P value of ≤0.05 in a Wilcoxon test and whose expression differed by a factor of ≥1.5 between the two growth conditions are listed. Genes are grouped according to function. Column two indicates protein function according to the SubtiList database (http://genolist.pasteur.fr/SubtiList/).

^bCells were grown in minimal medium (6 mM K₂HPO₄, 4.4 mM KH₂PO₄, 0.3 mM trisodium citrate, 5 mM MgCl₂, 0.5% glucose, 50 mg of l-tryptophan liter⁻¹, 22 mg of ferric ammonium citrate liter⁻¹, 0.1% l-glutamine) containing 1 mM sulfate or 1 mM methionine as the sulfur source. β-Galactosidase activities were determined in extracts prepared from exponentially growing cells. The values shown are averages from at least three independent experiments.