TABLE 1.
Genes with significantly higher expression during exponential growth of B. subtilis in minimal medium without CAA as revealed by transcriptome and proteome analysesa
| Gene and category | Function | Induction (expt 1, expt 2) | Transcriptional organization |
|---|---|---|---|
| Amino acid biosynthesis | |||
| argC | N-acetylglutamate gamma-semialdehyde dehydrogenase | 6.0, 3.8 | argC-argJ-argB-argD-carA-carB-argF |
| argJ | Ornithine acetyltransferase; amino acid acetyltransferase | 20.5, 11.6 | argC-argJ-argB-argD-carA-carB-argF |
| argB | N-acetylglutamate 5-phosphotransferase | 29.3, 34.2 | argC-argJ-argB-argD-carA-carB-argF |
| argD | N-acetylornithine aminotransferase | 4.7, 8.6 | argC-argJ-argB-argD-carA-carB-argF |
| carA | Carbamoyl-phosphate transferase (subunit A) | 30.0, 16.2 | argC-argJ-argB-argD-carA-carB-argF |
| carB | Carbamoyl-phosphate transferase (subunit B) | 4.6, 5.1 | argC-argJ-argB-argD-carA-carB-argF |
| argF | Ornithine carbamyoltransferase | 5.7, 9.6 | argC-argJ-argB-argD-carA-carB-argF |
| argG | Argininosuccinate synthase | 17.3, 23.9 | argG-argH-ytzD |
| argH | Argininosuccinate lyase | 21.4, 27.5 | argG-argH-ytzD |
| ytzD | Unknown function | —, — | argG-argH-ytzD |
| cysH | Phosphoadenosine phosphosulfate sulfotransferase | 3.3, 3.8 | cysH-cysP-sat-cysC-ylnD-ylnE-ylnF |
| cysP | Sulfate permease | 5.5, 3.3 | cysH-cysP-sat-cysC-ylnD-ylnE-ylnF |
| sat | Sulfate adenylyltransferase | 4.7, 4.6 | cysH-cysP-sat-cysC-ylnD-ylnE-ylnF |
| cysC | Adenylylsulfate kinase | 2.7, 4.7 | cysH-cysP-sat-cysC-ylnD-ylnE-ylnF |
| ylnD | Similar to uroporphyrine-III C-methyltransferase | 5.7, 5.2 | cysH-cysP-sat-cysC-ylnD-ylnE-ylnF |
| ylnE | Unknown function | 4.3, 3.1 | cysH-cysP-sat-cysC-ylnD-ylnE-ylnF |
| ylnF | Similar to uroporphyrine-III C-methyltransferase | 4.0, 3.6 | cysH-cysP-sat-cysC-ylnD-ylnE-ylnF |
| cysK | Cysteine synthase A | 2.0, 2.2 | cysK |
| hisZ | Histidyl-tRNA synthetase | —, — | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI |
| hisG | ATP phosphoribosyltransferase | —, 1.1 | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI |
| hisD | Histidinol dehydrogenase | 4.5, 7.2 | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI |
| hisB | Imidazoleglycerol-phosphate dehydratase | 5.7, 5.6 | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI |
| hisH | Amidotransferase | 5.2, 5.1 | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI |
| hisA | Phosphoribosylformimino-5-aminoimidazole carboxamideribotide isomerase | 5.5, 7.3 | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI |
| hisF | Cyclase-like protein (synthesis of imidazole glycerol phosphate) | 4.2, 6.6 | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI |
| hisI | Phosphoribosyl-ATP pyrophosphohydrolase; phosphribosyl-AMP cyclohydrolase | 8.5, 10.4 | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI |
| hom | Homoserine dehydrogenase | 2.2, 2.1 | hom-thrC-thrB |
| thrC | Threonine synthase | 2.0, 2.2 | hom-thrC-thrB |
| thrB | Homoserine kinase | 3.2, 3.5 | hom-thrC-thrB |
| ilyA | Threonine dehydratase | 3.9, 3.6 | ilvA-ypmP |
| ypmP | Unknown function | —, — | ilvA-ypmP |
| ilvB | Acetolactate synthase (large subunit) | 7.1, 7.9 | ilvB-ilvH-ilvC-leuA-leuB-leuC-leuD |
| ilvH | Acetolactate synthase (small subunit) | 11.0, 7.0 | ilvB-ilvH-ilvC-leuA-leuB-leuC-leuD |
| ilvC | Ketol-acid reductoisomerase | 9.9, 10.1 | ilvB-ilvH-ilvC-leuA-leuB-leuC-leuD |
| leuA | 2-Isopropylmalate synthase | 9.5, 9.7 | ilvB-ilvH-ilvC-leuA-leuB-leuC-leuD |
| leuB | 3-Isopropylmalate dehydrogenase | 9.6, 10.6 | ilvB-ilvH-ilvC-leuA-leuB-leuC-leuD |
| leuC | 3-Isopropylmalate dehydratase (large subunit) | 10.0, 10.9 | ilvB-ilvH-ilvC-leuA-leuB-leuC-leuD |
| leuD | 3-Isopropylmalate dehydratase (small subunit) | 7.0, 10.5 | ilvB-ilvH-ilvC-leuA-leuB-leuC-leuD |
| ilvD | Dihydroxyacid dehydratase | 4.6, 4.4 | ilvD |
| lvsC | Aspartokinase II (alpha and beta subunit) | 8.5, 13.4 | lysC |
| metE | Cobalamin-independent methionine synthase | 56.8, 59.9 | metC |
| ybgE | Similar to branched chain amino acid aminotransferase | 3.0, 4.1 | ybgE |
| yitJ | Similar to methionine synthase | 4.7, — | yitJ |
| yjcI | Similar to cystathionine gamma-synthase | 9.9, 6.9 | yjcI-yjcJ |
| yjcJ | Similar to cystathionine beta-lyase | 14.0, 9.9 | yjcI-yjcJ |
| yoaD | Similar to phosphoglycerate dehydrogenase | 3.1, — | yoaD-yoaC-yoaB |
| yoaC | Similar to xylulokinase | 2.5, 3.2 | yoaD-yoaC-yoaB |
| yoaB | Unknown function | 14.5, 9.2 | yoaD-yoaC-yoaB |
| yvgR | Similar to sulfite reductase | 2.1, 2.9 | yvgR-yvgQ |
| yvgQ | Similar to sulfite reductase | 5.0, 8.6 | yvgR-yvgQ |
| yxjG | Similar to methionine synthase | 10.5, 7.6 | yxjG |
| yxjH | Similar to methionine synthase | —, — | yxjH |
| Competence | |||
| comER | Nonessential gene for competence | 3.2, 3.4 | comER |
| comGA | Required for exogenous DNA binding | 2.0, 5.3 | comGA-comGB-comGC-comGD-comGE-comGF-comGG |
| comGB | Required for exogenous DNA binding | 2.2, 4.2 | comGA-comGB-comGC-comGD-comGE-comGF-comGG |
| comGC | Required for exogenous DNA binding | 3.2, 7.1 | comGA-comGB-comGC-comGD-comGE-comGF-comGG |
| comGD | Required for exogenous DNA binding | 3.0, 5.6 | comGA-comGB-comGC-comGD-comGE-comGF-comGG |
| comGE | Required for exogenous DNA binding | —, — | comGA-comGB-comGC-comGD-comGE-comGF-comGG |
| comGF | Required for exogenous DNA binding | 4.2, 4.2 | comGA-comGB-comGC-comGD-comGE-comGF-comGG |
| comGG | Required for exogenous DNA binding | 2.4, 4.3 | comGA-comGB-comGC-comGD-comGE-comGF-comGG |
| comK | Competence transcription factor | 3.1, 4.8 | comK |
| Transition state functions and sporulation | |||
| appD | Oligopeptide ABC transporter (ATP-binding protein) | —, — | appD-appF-appA-appB-appC |
| appF | Oligopeptide ABC transporter (ATP-binding protein) | 0.7, 0.9 | appD-appF-appA-appB-appC |
| appA | Oligopeptide ABC transporter (peptide-binding protein) | 21.9, 22.5 | appD-appF-appA-appB-appC |
| appB | Oligopeptide ABC transporter (permease) | —, 5.7 | appD-appF-appA-appB-appC |
| appC | Oligopeptide ABC transporter (permease) | —, — | appD-appF-appA-appB-appC |
| cotE | Spore coat protein | 13.5, 5.8 | cotE |
| cotV | Spore coat protein | 6.1, — | cotV-cotW-cotX |
| cotW | Spore coat protein | 3.5, 3.5 | cotV-cotW-cotX |
| cotX | Spore coat protein | 7.5, — | cotV-cotW-cotX |
| dacF | Penicillin binding protein; required for spore cortex synthesis | 4.6, 2.4 | dacF-spoIIAA-spoIIAB-sigF |
| spoIIAA | Anti-anti-sigma factor (antagonist of SpoIIAB) | 0.9, 0.9 | dacF-spoIIAA-spoIIAB-sigF |
| spoIIAB | Anti-sigma factor (antagonist of sigma F); serine kinase | —, — | dacF-spoIIAA-spoIIAB-sigF |
| sigF | RNA polymerase sporulation-specific sigma factor | 5.9, 5.3 | dacF-spoIIAA-spoIIAB-sigF |
| gerM | Germination (cortex hydrolysis) and sporulation (putative role in peptidoglycan synthesis) | 3.3, 3.8 | gerM |
| prkA | Serine protein kinase | 2.5, 2.5 | prkA |
| qcrA | Menaquinol:cytochrome c oxidoreductase (iron-sulfur subunit) | 4.1, 4.0 | qcrA-qcrB-qcrC |
| qcrB | Menaquinol:cytochrome c oxidoreductase (cytochrome b subunit) | —, — | qcrA-qcrB-qcrC |
| qcrC | Menaquinol:cytochrome c oxidoreductase (cytochrome c subunit) | 3.1, 5.3 | qcrA-qcrB-qcrC |
| rapA | Aspartyl phosphate phosphatase | 3.2, 3.4 | rapA-phrA |
| phrA | Inhibitor of the activity of phosphatase RapA | 4.1, 1.8 | rapA-phrA |
| rsfA | Probable transcriptional regulator of sigma F-dependent genes | 4.5, 4.2 | rsfA |
| sp0A | Two-component response regulator | 2.9, 2.5 | spo0A |
| spoIIB | Required for endospore development | 6.4, 3.7 | spoIIB |
| spoIIIAG | Mutants block sporulation after engulfment | 5.5, 4.3 | spoIIIAG-spoIIIAH |
| spoIIIAH | Mutants block sporulation after engulfment | 7.8, 4.3 | spoIIIAG-spoIIIAH |
| usd | Required for translation of spoIIID | —, — | usd-spoIIID |
| spoIIID | Transcriptional regulator of sigma E- and sigma K-dependent genes | 10.2, 4.7 | usd-spoIIID |
| spoIVA | Required for proper spore cortex formation and coat assembly | 2.4, 2.5 | spoIVA |
| spoVID | Required for assembly of the spore coat | 3.2, 3.5 | spoVID-ysxE |
| ysxE | Unknown function | —, — | spoVID-ysxE |
| sspE | Small acid-soluble spore protein | 4.3, 2.5 | sspE |
| yjbX | Unknown function; glutamic acid-rich protein | 7.2, 6.2 | yjbX |
| ylaK | Similar to phosphate starvation inducible protein | 6.5, 4.7 | ylaK |
| ylbO | Unknown function | 6.8, 3.0 | ylbO |
| yqxM | Unknown function | 0.9, 1.1 | yqxM-sipW-tasA |
| sipW | Type I signal peptidase | 0.9, 1.3 | yqxM-sipW-tasA |
| tasA | Spore-associated antimicrobial protein required for spore coat assembly | 2.0, 3.1 | yqxM-sipW-tasA |
| ytfI | Unknown function | —, — | ytfI-ytfJ |
| ytfJ | Unknown function | 3.7, 3.8 | ytfI-ytfJ |
| yuiC | Unknown function | 3.1, 3.0 | yuiC |
| ywcI | Unknown function | 10.1, 7.3 | ywcI-sacT |
| sacT | Transcriptional antiterminator (regulation of the sacP operon) | 9.9, 6.4 | ywcI-sacT |
| yvyD | Similar to a sigma 54 modulating factor | 2.4, 3.4 | yvyD |
| Other functions | |||
| dat | Probable d-alanine aminotransferase | 1.5, 1.7 | dat |
| gcvT | Probable aminomethyltransferase | 1.9, 1.9 | gcvT-gcvPA-gcvPB |
| gcvPA | Probable glycine decarboxylase (subunit 1) | 2.8, 2.6 | gcvT-gcvPA-gcvPB |
| gcvPB | Probable glycine decarboxylase (subunit 2) | 2.4, 2.6 | gcvT-gcvPA-gcvPB |
| mpr | Extracellular metalloprotease | 6.6, 3.2 | mpr-ybfJ |
| ybfJ | Unknown function | —, — | mpr-ybfJ |
| yfhK | Similar to cell division inhibitor | 3.2, 6.5 | yfhK |
| yhgB | Unknown function | —, — | yhgB-yhfA-yhaA |
| yhfA | Unknown function | —, — | yhgB-yhfA-yhaA |
| yhaA | Similar to aminoacylase | 4.2, 4.5 | yhgB-yhfA-yhaA |
| ykrT | Unknown function | 1.6, 1.7 | ykrT-ykrS |
| ykrS | Similar to initiation factor eIF-2B (alpha subunit) | 2.5, 3.5 | ykrT-ykrS |
| ykrW | Similar to ribulose-bisphosphate carboxylase | 2.7, 3.3 | ykrW-ykrX-ykrY-ykrZ |
| ykrX | Unknown function | 3.9, 4.9 | ykrW-ykrX-ykrY-ykrZ |
| ykrY | Unknown function | 6.8, 4.8 | ykrW-ykrX-ykrY-ykrZ |
| ykrZ | Unknown function | 3.1, 2.1 | ykrW-ykrX-ykrY-ykrZ |
| ykuN | Similar to flavodoxin | —, — | ykuN-ykuO-ykuP-ykuQ |
| ykuO | Unknown function | 2.8, 2.9 | ykuN-ykuO-ykuP-ykuQ |
| ykuP | Similar to flavodoxin | 4.7, 3.5 | ykuN-ykuO-ykuP-ykuQ |
| ykuQ | Similar to tetrahydrodipicolinate succinylase | 0.9, 1.3 | ykuN-ykuO-ykuP-ykuQ |
| ykwC | Similar to 3-hydroxyisobutyrate dehydrogenase | 1.7, 1.9 | ykwC |
| yodF | Similar to proline permease | 4.5, 4.4 | yodF |
| yojA | Similar to gluconate permease | —, — | yojA-yojB-yojC |
| yojB | Unknown function | 3.8, 3.9 | yojA-yojB-yojC |
| yojC | Unknown function | —, — | yojA-yojB-yojC |
| yqiX | Similar to amino acid ABC transporter (binding protein) | 7.3, 10.3 | yqiX-yqiY-yqiZ |
| yqiY | Similar to amino acid ABC transporter (permease) | 5.3, 7.1 | yqiX-yqiY-yqiZ |
| yqiZ | Similar to amino acid ABC transporter (ATP binding) | 7.1, 16.0 | yqiX-yqiY-yqiZ |
| yuaF | Unknown function | —, — | yuaF-yuaG-yuaI |
| yuaG | Similar to epidermal surface antigen | 3.4, 3.1 | yuaF-yuaG-yuaI |
| yuaI | Unknown function | —, — | yuaF-yuaG-yuaI |
| yvaC | Unknown function | —, — | yvaC-yvaB |
| yvaB | Similar to NAD(P)H dehydrogenase (quinone) | 2.3, 1.7 | yvaC-yvaB |
| ywfH | Similar to 3-oxoacyl-acyl-carrier protein reductase | 3.8, 3.2 | ywfH |
| Unknown functions | |||
| ybdO | Unknown function | 3.2, 7.2 | ybdO |
| yfhB | Unknown function | 3.7, 3.0 | yfhB |
| yfmA | Unknown function | —, — | yfmA-yflT |
| yflT | Unknown function | 4.6, 40.9 | yfmA-yflT |
| yjcE | Unknown function | 3.8, 3.6 | yjcE-yjcD |
| yjcD | Similar to ATP-dependent DNA helicase | 0.7, 1.4 | yjcE-yjcD |
| yjcH | Unknown function | 1.7, 3.1 | yjcH-yjcG-yjcF |
| yjcG | Unknown function | 3.7, 3.6 | yjcH-yjcG-yjcF |
| yjcF | Unknown function | 2.4, 1.8 | yjcH-yjcG-yjcF |
| ykvR | Unknown function | 3.2, 3.3 | ykvR |
| ylaJ | Unknown function | 3.1, 3.0 | ylaJ |
| ylqB | Unknown function | 3.3, 3.8 | ylqB |
| yqgZ | Unknown function | 4.6, 3.4 | yqgZ |
| yvaW | Unknown function | —, — | yvaW-yvaX-yvaY |
| yvaX | Unknown function | —, — | yvaW-yvaX-yvaY |
| yvaY | Unknown function | 10.6, 12.2 | yvaW-yvaX-yvaY |
a
Significantly regulated genes are given in bold face. Significant regulation was defined as at least threefold changes in the mRNA levels in both macroarray experiments. Genes were also regarded as significantly regulated when at least twofold changes in the mRNA levels were confirmed by the proteome analysis or the operon structure. Underlined gene names indicate higher expression in minimal medium without CAA as revealed by the proteome analysis. The calculated expression level ratios are shown for both independent macroarray experiments in the column “induction,” whereby dashes indicate that specific signals for these genes were below the significance threshold. The putative functions of the y-gene-encoded proteins were obtained from the SubtiList database.