TABLE 1.

Transcript levels of genes involved in biosynthesis of riboflavin, biotin, and thiamine

Biosynthesis type and genea	Enzyme and/or functiona	Ratiob
		wt−/wt+c	deg+/wt+
Riboflavin
ribG	Riboflavin-specific deaminase or reductase	2.0	12
ribB	Riboflavin synthase (α subunit)	2.5	28
ribA	GTP cyclohydrolase IV 3,4-dihydroxy-2-butanone 4-phosphate synthase	2.9	19
ribH	Lumazine synthase (β subunit)	2.7	13
ribT	Unknown (not required for riboflavin synthesis)	NC	NC
ribC	Riboflavin kinase or FAD synthase	NC	NC
ribR	Cryptic riboflavin kinase	NT	NT
ypaA	Unknown transmembrane protein	NC	11
Biotin
bioW	Pimeloyl-CoA synthase	89	>100
bioA	DAPA aminotransferase	>100	>100
bioF	7-KAP synthase	52	60
bioD	DTB synthetase	48	86
bioB	Biotin synthase	94	>100
bioI	Biotin cytochrome P-450	33	66
ytbQ	Unknown and/or not required for biotin synthesis	62	100
birA	Biotin operon repressor/biotin-protein ligase	NC	NC
yuiG	Unknown function or homologous to B. sphaericus bioY	21	17
yhfU	Unknown function or homologous to B. sphaericus bioY	11	16
Thiamine
thiA	Biosynthesis of hydroxymethylpyrimidine phosphate	62
thiK	Hydroxyethylthiazole kinase	NC
thiC	Thiamine phosphate pyrophosphorylase	NC
goxB	Glycine oxidase; possible thiO ortholog	67
thiS (yjbS)	Biosynthesis of hydroxyethylthiazole phosphate	84
thiG (yjbT)	Biosynthesis of hydroxyethylthiazole phosphate	82
thiF (yjbU)	Biosynthesis of hydroxyethylthiazole phosphate	90
thiD (yjbV)	Possible phosphomethylpyrimidine kinase	32
ydiA	Unknown; possible thiL ortholog (TMP kinase)	NC
ytbJ	Unknown; possible thiI ortholog (sulfur transferase)	NC
dxs (yqiE)	1-Deoxy-d-xylulose synthase	NC

^aGene names and functions are as described in Perkins and Pero (27) and SubtiList (http://genolist.pasteur.fr/SubtiList). Abbreviations: CoA, coenzyme A; FAD, flavin adenine dinucleotide; DAPA, 7,8-diaminopelargonic acid; DTB, dethiobiotin; 7-KAP, 7-keto-8-aminopelargonic acid; TMP, thiamine monophosphate. 

^bTranscript ratios were calculated by dividing the average difference values (after normalization) from hybridization experiments of wild-type cells grown to exponential phase in minimal medium without vitamin treatment by those with vitamin treatment (wt−/wt+) or from hybridization experiments of deregulated mutant cells grown to exponential phase in minimal medium with vitamin treatment by those of wild-type cells grown under the same condition (deg+/wt+). B. subtilis BI421 (birA) was used in the biotin treatment experiments, and B. subtilis BS0012 (ribC) was used in the riboflavin treatment experiments. For some genes (indicated in boldface), average difference values were obtained from duplicate probe sets per hybridization experiment. NC, no change in average difference values; NT, no transcript detected. 

^cAverage of two independent experiments. r values (vitamin-treated versus untreated datasets) for experiments 1 and 2: biotin, 0.91 and 0.89; thiamine, 0.94 and 0.95; and riboflavin, 0.90 and 0.90, respectively.