Table 3.
Transcriptome analysis for definition of YvoA (NagR) regulon in B. subtilisa
| Category and KEGG no. | Name(s) | Function | Expression, ΔyvoA/wt | cis-acting element | Pathway | Regulon(s) | Reference(s) | |
|---|---|---|---|---|---|---|---|---|
| Genes upregulated in the ΔyvoA mutant compared to parental strain B. subtilis WH558 | ||||||||
| BSU07700 | nagP | PTS N-acetylglucosamine-specific enzyme IICB component | +4.55 | YvoA | GlcNAc metabolism | YvoA | This study | |
| BSU35010 | nagA | N-Acetylglucosamine-6-phosphate deacetylase | +2.53 | YvoA | GlcNAc metabolism | YvoA | This study | |
| BSU04300 | ydaM | Putative glycosyltransferase associated to biofilm formation | +3.95 | — | Biofilm formation | — | — | |
| BSU33950 | cggR | Central glycolytic genes repressor | +3.49 | CggR | Glycolysis | CggR | 31 | |
| BSU15510 | pyrAA | Carbamoyl phosphate synthase small subunit | +2.85 | PyrR | Pyrimidine biosynthesis | PyrR | 25 | |
| BSU15520 | pyrAB | Carbamoyl phosphate synthase large subunit | +3.44 | PyrR | Pyrimidine biosynthesis | PyrR | 25 | |
| BSU15500 | pyrC | Dihydroorotase | +2.35 | PyrR | Pyrimidine biosynthesis | PyrR | 25 | |
| BSU15540 | pyrD | Dihydroorotate dehydrogenase 1B | +2.30 | PyrR | Pyrimidine biosynthesis | PyrR | 25 | |
| BSU15560 | pyrE | Orotate phosphoribosyltransferase | +2.21 | PyrR | Pyrimidine biosynthesis | PyrR | 25 | |
| BSU15550 | pyrF | Orotidine 5′-phosphate decarboxylase | +2.23 | PyrR | Pyrimidine biosynthesis | PyrR | 25 | |
| BSU15530 | pyrK | Dihydroorotate dehydrogenase electron transfer subunit | +2.24 | PyrR | Pyrimidine biosynthesis | PyrR | 25 | |
| BSU02700 | lip, estA | Secreted triacylglycerol alkaliphilic lipase | +2.01 | — | Triacylglycerol metabolism | — | 15 | |
| BSU37210 | ywjC | Hypothetical protein | +2.60 | — | Unknown function | — | — | |
| Genes downregulated in the ΔyvoA mutant compared to parental strain B. subtilis WH558 | ||||||||
| BSU37310 | fnr | Fnr, fumarate nitrate reductase regulator | −2.63 | Fnr | Anaerobic redox regulator | Fnr | 14 | |
| BSU37290 | arfM | Anaerobic respiration and fermentation modulator | −4.10 | Fnr | Anaerobic genes regulator | Fnr/ResDE | 35 | |
| BSU37300 | ywiC | Unknown, putative integral inner membrane protein | −4.13 | Fnr | Unknown | — | — | |
| BSU37280 | narG | Nitrate reductase (alpha subunit) | −2.70 | Fnr | Nitrate reduction | Fnr | 14 | |
| BSU37270 | narH | Nitrate reductase (beta subunit) | −3.13 | Fnr | Nitrate reduction | Fnr | 14 | |
| BSU37250 | narI | Nitrate reductase assembling factor | −3.17 | Fnr | Nitrate reduction | Fnr | 14 | |
| BSU37260 | narJ | Nitrate reductase (gamma subunit) | −2.62 | Fnr | Nitrate reduction | Fnr | 14 | |
| BSU37320 | narK | Nitrite extrusion permease | −3.84 | Fnr | Nitrate extrusion | Fnr | 14 | |
| BSU14160 | ykuO | Hypothetical protein | −5.13 | Fur | Flavodoxins for NO production | Fnr/Fur | 3, 47 | |
| BSU14170 | ykuP | Short-chain flavodoxin | −3.99 | Fur | Flavodoxins for NO production | Fnr/Fur | 3, 47 | |
| BSU32000 | dhbA | 2.3-Dihydroxybenzoate-2.3-dehydrogenase | −4.26 | Fur | Siderophore (Bacillibactin) synthesis | Fnr/Fur | 3, 47 | |
| BSU31970 | dhbB | Isochorismatase | −3.58 | Fur | Siderophore (Bacillibactin) synthesis | Fnr/Fur | 3, 47 | |
| BSU31990 | dhbC | Isochorismate synthase | −2.99 | Fur | Siderophore (Bacillibactin) synthesis | Fnr/Fur | 3, 47 | |
| BSU31980 | dhbE | 2.3-Dihydroxybenzoate-AMP ligase | −3.64 | Fur | Siderophore (Bacillibactin) synthesis | Fnr/Fur | 3, 47 | |
| BSU31960 | dhbF | Siderophore 2.3-dihydroxybenzoate-glycine-threonine trimeric ester | −4.91 | Fur | Siderophore (Bacillibactin) synthesis | Fnr/Fur | 3, 47 | |
| BSU38740 | cydC | ABC transporter (ATP-binding) for cytochrome bd function | −3.32 | YdiH | Low oxygen tension | Fnr/Fur/YdiH | 59 | |
| BSU22070 | xpt | Xanthine phosphoribosyltransferase | −2.59 | — | Purine biosynthesis | — | — | |
| BSU02420 | ybgH, glnT | Glutamine transporter | −2.39 | GlnL | Gln/Glu metabolism | GlnL | 58 | |
| BSU01640 | ybbB, Btr | Bacillibactin transport regulator | −2.38 | Fur | Bacillibactin uptake | Fur | 3 | |
| BSU37410 | albE | Putative hydrolase involved in subtilosin production | −2.02 | AbrB/ResD | Antilisterial bacteriocin (subtilosin) production | ResD/Fnr/AbrB/Spo0A | 69 | |
| BSU37420 | albF | Putative peptidase involved in subtilosin production | −2.37 | AbrB/ResD | Antilisterial bacteriocin (subtilosin) production | ResD/Fnr/AbrB/Spo0A | 69 | |
| BSU01630 | feuA | Iron hydroxamate-binding lipoprotein | −2.27 | Fur | Siderophore uptake | Fur | 3 | |
| BSU01620 | feuB | Iron-uptake protein | −2.00 | Fur | Siderophore uptake | Fur | 3 | |
| BSU01610 | feuC | Iron-uptake protein | −2.02 | Fur | Siderophore uptake | Fur | 3 | |
| BSU32940 | yusV | Iron(III)-siderophore transporter | −2.10 | Fur | Siderophore uptake | Fur | 3 | |
| BSU33320 | fhuD | Ferrichrome ABC transporter | −2.04 | Fur | Siderophore uptake | Fur | 3 | |
| BSU39610 | yxeB | ABC transporter (ferrioxamine binding lipoprotein) | −2.21 | Fur | Siderophore uptake | Fur | 3 | |
| BSU04530 | ydbN | Hypothetical protein | −2.02 | Fur | Unknown function | Fnr/Fur | 3, 47 | |
| BSU32030 | yuiG, bioYB | Putative biotin transporter | −3.77 | — | — | — | — | |
| BSU36550 | spoIIQ | Forespore protein required for alternative engulfment | −2.21 | — | Spore engulfment | — | 30 | |
| BSU34140 | yvfM, ganQ | Arabinogalactan oligomer permease | −2.20 | — | Arabinogalactan metabolism | — | — | |
| BSU30280 | amyD | Carbohydrate ABC transporter | −2.16 | — | Carbohydrate metabolism | — | — | |
| BSU19310 | dhaS | Putative aldehyde dehydrogenase | −2.12 | — | Unknown | — | — | |
| BSU11990 | yjdB | Hypothetical protein | −2.01 | — | Unknown function | — | — |
a
—, cis-acting element, trans-acting regulator, pathway, or regulon unknown. Genes listed exhibited differential expression by a factor of at least 2, with a Cyber-T (Bayes) P value of <0.01 (see Materials and Methods), between WH558 and FT20 grown without GlcNAc.