Table 1. Selected induced genes and proteins.
| ORF ID | gene | transcriptome | proteome | Regulon in other Bacilli | |||
| 3 min | 8 min | 10 min | 30 min | ||||
| BPJ13600 | zinc-transporting ATPase ZosA | zosA | 12.74 | 28.72 | perR | ||
| BPJ25410 | glutamyl-tRNA reductase HemA | hemA | 3.44 | 3.99 | perR | ||
| BPJ25390 | porphobilinogen deaminase HemC | hemC | 2.68 | 3.90 | perR | ||
| BPJ25370 | delta-aminolevulinic acid dehydratase HemB | hemB | 2.52 | 3.72 | perR | ||
| BPJ25400 | putative cytochrome C biogenesis protein HemX | hemX | 2.86 | 4.25 | perR | ||
| BPJ25380 | uroporphyrinogen III synthase HemD | hemD2 | 2.68 | 4.23 | perR | ||
| BPJ25360 | glutamate-1-semialdehyde 2,1-aminomutase HemL | hemL | 2.75 | 3.56 | perR | ||
| BPJ21690 | Fur family ferric uptake regulation protein Fur | fur | 1.92 | 3.62 | perR | ||
| BPJ11620 | transcriptional regulator Spx | spxA | 4.14 | 3.31 | perR/spx/sigB | ||
| BPJ11610 | putative N-acetyltransferase YjbC | yjbC | 2.41 | 4.41 | perR/spx/sigB/sigM/sigW/sigX | ||
| BPJ09760 | catalase KatX2 | katX2 | 6.96 | 10.69 | 15.18 | 21.09 | sigB/sigF |
| BPJ34450 | putative ABC transporter permease YwjA | ywjA | 1.57 | 4.47 | fur | ||
| BPJ30810 | hydroxamate siderophore ABC transporter ATP-bindingprotein FhuC | fhuC1 | 1.51 | 2.46 | fur | ||
| BPJ30830 | hydroxamate siderophore ABC transporter permeaseFhuB | fhuB1 | 1.52 | 4.01 | fur | ||
| BPJ30820 | hydroxamate siderophore ABC transporter permeaseFhuG | fhuG1 | 1.53 | 3.20 | fur | ||
| BPJ08440 | ABC transport system permease | bpj08440 | 4.11 | 7.49 | fur | ||
| BPJ08430 | putative iron complex transport system substratebinding protein | bpj08430 | 4.54 | 7.43 | fur | ||
| BPJ08420 | putative HTH-type transcriptional regulator | bpj08420 | 3.58 | 5.59 | fur | ||
| BPJ08580 | putative nitroreductase YfhC | yfhC | 2.67 | 5.00 | 1.10 | fur | |
| BPJ08410 | ferredoxin–NADP reductase 2 | bpj08410 | 3.90 | 3.83 | fur | ||
| BPJ37570 | AraC family transcriptional regulator/putativeFeuA-like substrate-binding domain ybbB | ybbB | 4.93 | 12.84 | fur | ||
| BPJ37580 | iron complex ABC transporter substrate-binding proteinFeuA | feuA | 3.21 | 10.04 | fur, btr, citB | ||
| BPJ37590 | putative bacillibactin esterase YbbA | ybbA | 5.24 | 18.42 | fur/btr/citB | ||
| BPJ07970 | C56 family peptidase YfkM | yfkM | 2.94 | 7.61 | 7.39 | 3.09 | fur/sigB |
| RBPU30260 | FeS cluster assembly protein SufB | sufB | 1.87 | 2.10 | 1.73 | Fe/S cluster biogenesis | |
| RBPU30280 | cysteine desulfurase SufS | sufS | −1.77 | 2.69 | Fe/S cluster biogenesis | ||
| RBPU30290 | FeS cluster assembly permease SufD | sufD | 1.73 | Fe/S cluster biogenesis | |||
| RBPU30300 | FeS cluster assembly ATPase SufC | sufC | 2.52 | 2.13 | Fe/S cluster biogenesis | ||
| BPJ11040 | diaminobutyrate–2-oxoglutarate aminotransferase RhbA | rhbA | −1.11 | 11.10 | siderophore synthesis | ||
| BPJ11080 | rhizobactin siderophore biosynthesis protein RhbE | rhbE | −1.18 | 5.28 | siderophore synthesis | ||
| BPJ11090 | rhizobactin siderophore biosynthesis protein RhbF | rhbF | −1.72 | 3.02 | siderophore synthesis | ||
| BPJ35800 | iron complex ABC transporter ATP-binding protein FhuC | fhuC2 | 3.88 | 7.85 | iron uptake | ||
| BPJ35810 | iron complex ABC transporter permease FhuB | fhuB2 | 3.32 | 7.15 | iron uptake | ||
| BPJ35770 | putative iron complex ABC transporter permease FhuG | fhuG2 | 2.31 | 4.39 | iron uptake | ||
| BPJ35780 | putative iron complex ABC transporter substrate-binding protein FhuD | fhuD | 2.72 | 5.57 | iron uptake | ||
| BPJ35830 | putative iron transport-associated protein/putative siderophore | bpj35830 | 3.65 | 5.84 | iron uptake | ||
| BPJ35840 | putative heme uptake protein IsdC | bpj35840 | 4.91 | 7.62 | iron uptake | ||
| BPJ35850 | putative iron transport-associated protein | bpj35850 | 3.89 | 6.47 | iron uptake | ||
| BPJ28430 | DinB-like domain-containing protein YuaE | yuaE | 2.25 | 2.87 | spx | ||
| BPJ31980 | thioredoxin-disulfide reductase TrxB | trxB | 3.97 | 3.93 | 3.59 | spx | |
| BPJ29110 | putative NADH-dependent butanol dehydrogenase YugJ | yugJ | 2.32 | 1.08 | 4.60 | spx | |
| BPJ19830 | methionine sulfoxide reductase MsrA | msrA | 1.46 | 2.24 | spx | ||
| BPJ19820 | peptide-methionine sulfoxide reductase MsrB | msrB | 1.48 | 2.27 | spx | ||
| BPJ25870 | thioredoxin TrxA | trxA | 1.40 | 2.58 | spx/ctsR/sigB | ||
| BPJ35200 | NADPH-dependent nitro/flavin reductase NfrA | nfrA | 2.50 | 2.47 | 5.21 | spx/sigD/spo0A | |
| BPJ24450 | cystathionine gamma-lyase MccB | mccB | −1.58 | 7.58 | spx/cymR | ||
| BPJ17710 | putative cell division suppressor protein YneA | yneA | 2.24 | 44.25 | lexA/SOS | ||
| BPJ10180 | 3′-5′ exoribonuclease YhaM | yhaM | 0.71 | 2.81 | lexA/SOS | ||
| BPJ21860 | DNA polymerase 4 | polY1 | 10.68 | lexA/SOS | |||
| BPJ32300 | excinuclease ABC subunit B | uvrB | 7.22 | 2.52 | 4.29 | lexA/SOS | |
| BPJ32290 | excinuclease ABC subunit A | uvrA | 1.49 | 6.75 | lexA/SOS | ||
| BPJ25860 | excinuclease ABC subunit UvrC | uvrC | 3.65 | lexA/SOS | |||
| BPJ17700 | repressor LexA | lexA | 1.55 | 5.66 | lexA/SOS | ||
| BPJ17730 | DUF896 family protein YnzC | ynzC | 0.65 | 8.85 | lexA/SOS | ||
| BPJ12460 | phage-like PBSX protein XkdA | xkdA | 3.10 | 17.84 | lexA/SOS | ||
| BPJ17720 | resolvase-like protein YneB | yneB | 1.38 | 17.03 | lexA/SOS | ||
| BPJ10160 | putative exonuclease YhaO | yhaO | 8.76 | lexA/SOS | |||
| BPJ16880 | recombinase RecA | recA | 1.63 | 7.22 | 4.94 | 9.58 | lexA/SOS/comK |
| BPJ35170 | minor extracellular serine protease Vpr | vpr | 1.58 | 2.23 | lexA/SOS/phoP | ||
| BPJ21470 | hypothetical protein YpuD | ypuD | 1.93 | 7.12 | lexA/SOS/sigB/sigM | ||
| BPJ10170 | putative ATPase YhaN | yhaN | 8.73 | lexA/SOS | |||
| BPJ13450 | ATP-dependent Clp protease ATP-binding subunit ClpE | clpE | 2.78 | 45.41 | ctsR | ||
| BPJ25460 | ATP-dependent protease ATP-binding subunit ClpX | clpX | 2.67 | ctsR | |||
| BPJ00800 | DNA repair protein RadA | radA | 10.02 | ctsR/sigB | |||
| BPJ00760 | transcriptional regulator CtsR | ctsR | 9.40 | ctsR/sigB | |||
| BPJ00770 | transcriptional regulator McsA | mcsA | 10.26 | ctsR/sigB | |||
| BPJ31850 | ATP-dependent Clp protease proteolytic subunit ClpP | clpP | 1.79 | 4.26 | 8.74 | 1.73 | ctsR/sigB |
| BPJ00780 | putative ATP:guanido phosphotransferase McsB | mcsB | 1.43 | 8.87 | ctsR/sigB/sigF | ||
| BPJ00790 | ATP-dependent Clp protease ClpC | clpC | 6.44 | ctsR/sigB/sigF | |||
| BPJ00810 | DNA integrity scanning protein DisA | disA | 5.15 | ctsR/sigB/sigM | |||
| BPJ15470 | adenylyl-sulfate kinase CysC | cysC | 23.93 | 1.60 | cymR | ||
| BPJ15480 | uroporphyrin-3 C-methyltransferase CysG | cysG | 1.49 | 10.53 | cymR | ||
| BPJ15460 | sulfate adenylyltransferase Sat | sat | 1.37 | 13.07 | cymR | ||
| BPJ20800 | tryptophan synthase alpha subunit TrpA | trpA | 2.16 | 13.51 | TRAP | ||
| BPJ20810 | tryptophan synthase beta subunit TrpB | trpB | 1.13 | 13.99 | TRAP | ||
| BPJ20820 | N-(5′-phosphoribosyl)anthranilate isomerase TrpF | trpF | 1.59 | 2.09 | TRAP | ||
| BPJ20830 | indole-3-glycerol-phosphate synthase TrpC | trpC | 2.36 | 1.49 | 10.53 | TRAP | |
| BPJ20840 | anthranilate phosphoribosyltransferase TrpD | trpD | 1.44 | 2.72 | 1.37 | 13.07 | TRAP |
| BPJ20850 | anthranilate synthase component 1 | trpE | 2.61 | TRAP | |||
| BPJ12980 | transcriptional regulator OhrR | ohrR | 2.54 | ohrR | |||
| BPJ12970 | peroxiredoxin OhrA | ohrA | 10.66 | 9.88 | 6.29 | 1.30 | ohrR |
| BPJ12990 | peroxiredoxin OhrB | ohrB | 2.10 | sigB/ohrR | |||
| BPJ19510 | putative bacillithiol biosynthesis deacetylase YojG | yojG | 3.31 | bacillithiol-related | |||
| BPJ20020 | DUF1094 family protein YphP | yphP | 1.78 | 2.22 | bacillithiol-related | ||
| BPJ21140 | putative thioredoxin reductase YpdA | ypdA | 0.67 | 2.58 | bacillithiol-related | ||
| BPJ22220 | DUF1094 family protein YqiW | yqiW | 2.58 | bacillithiol-related | |||
| BPJ31300 | glycine betaine/carnitine/choline ABC transporter permease OpuCD | opuCD | 3.03 | glycine betaine transport | |||
| BPJ31310 | glycine betaine/carnitine/choline ABC transporter substrate-binding protein OpuCC | opuCC | 0.88 | 2.62 | glycine betaine transport | ||
| BPJ31320 | glycine betaine/carnitine/choline ABC transporter permease OpuCB | opuCB | 0.92 | 2.74 | glycine betaine transport | ||
| BPJ31330 | glycine betaine/carnitine/choline ABC transporter ATP-binding protein OpuCA | opuCA | 0.94 | 2.46 | glycine betaine transport | ||
| BPJ02950 | glycine betaine ABC transporter ATP-binding protein OpuAA | opuAA | 2.76 | 10.75 | glycine betaine transport | ||
| BPJ02960 | glycine betaine ABC transporter membrane protein | opuAB | 2.41 | 10.19 | glycine betaine transport | ||
| BPJ02970 | glycine betaine ABC transporter substrate-binding protein | opuAC | 2.37 | 7.48 | glycine betaine transport | ||
| BPJ29360 | Na+/H+ antiporter subunit MrpA | mrpA | 4.57 | sodium transport | |||
| BPJ29370 | Na+/H+ antiporter subunit MrpB | mrpB | 4.77 | sodium transport | |||
| BPJ29380 | Na+/H+ antiporter subunit MrpC | mrpC | 3.60 | sodium transport | |||
| BPJ29390 | Na+/H+ antiporter subunit MrpD | mrpD | 1.48 | 3.87 | sodium transport | ||
| BPJ29400 | Na+/H+ antiporter subunit MrpE | mrpE | 1.51 | 3.20 | sodium transport | ||
| BPJ29410 | Na+/H+ antiporter subunit MrpF | mrpF | 1.72 | 3.38 | sodium transport | ||
| BPJ29420 | Na+/H+ antiporter subunit MrpG | mrpG | 1.96 | 2.60 | sodium transport | ||
Selected genes and proteins that are induced in H2O2 treated B. pumilus cells.
Genes and proteins are listed, which could be assigned to putative regulons known from other Bacilli. Complete lists of upregulated as well as downregulated genes/proteins is given in supporting information Tables S2 and S3. For transcriptome, selected genes are shown for 3 and 8 minutes after stress compared to the control conditions (0 min). For a complete list of induced and repressed genes see Table S3. Differential regulation was determined from the biological triplicate measurements by false-discovery rate (FDR) from the Cyber-T p-values [27] by means of multiple testing correction [26]. Differential regulation was defined as a two-fold or higher differential expression with a FDR cut-off value of 0.05 or lower. Protein quantification was performed by the Delta 2D software (Decodon) from 3 biological replicates with a FDR cut-off value of 0.05 or lower.