Supporting Information for Proteomics DOI 10.1002/pmic.200300752 Haike Antelmann, Ron Sapolsky, Brian Miller, Eugenio Ferrari, Gopal Chotani, Walter Weyler, Alfred Gaertner and Michael Hecker Quantitative proteome profiling during the fermentation process of pleiotropic Bacillus subtilis mutants ª 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de Fermentation proteome profiling Antelmann et al. Table I Classification of proteins identified on the cytoplasmic proteome of the B. subtilis parental strain BG2822 grown in 2x SNB medium according to the SubiList code SubtiLi fun,cat protein st acc. function or homology, EC code, avgX avgY a) b) c) d) e) f) name no. synonym pI Mw 1,1 GcaD BG10113 173,5 173,8 5,65 49290 UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) 1,1 GtaB BG10402 UDP-glucose pyrophosphorylase (EC 2.7.7.9.) 338,8 316,3 4,91 32917 1,1 MurA BG11955 UDP-N-acetylglucosamine 1-carboxyvinyl transferase (EC 229,0 209,2 5,45 46537 2.5.1.7) 1,1 MurE BG10223 UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate 184,4 171,7 5,56 54157 ligase (EC 6.3.2.13) 1,1 MurF BG12084 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate- 197,9 185,6 5,33 49557 D-alanyl-D-alanyl ligase (EC 6.3.2.15) 1,2 OppA BG10771 oligopeptide ABC transporter (binding protein) 264,1 165,7 5,72 61318 1,2 OppD BG10774 oligopeptide ABC transporter (ATP-binding protein) 124,6 223,3 6,02 39606 1,2 RbsB BG10881 ribose ABC transporter (ribose-binding protein) 6.14 32073 1,2 YciC BG12021 probably part of a low-affinity pathway of zinc transport 4,40 45145 1,2 YqiX BG11727 similar to amino acid ABC transporter (binding protein) 373,0 359,3 5,09 28162 1,2 YurY BG14011 similar to ABC transporter (ATP-binding protein) 402,5 344,7 4,62 28879 1,2 YvdG BG12416 similar to maltose/maltodextrin-binding protein 387,0 212,1 4,91 45437, 1,4 AtpA BG10819 ATP synthase alpha chain (EC 3.6.1.34) 318,3 182,7 5,04 54432 1,4 AtpD BG10821 ATP synthase beta chain (EC 3.6.1.34) 423,1 191,0 4,61 51255 1,4 AtpF BG10817 ATP synthase (subunit b) (EC 3.6.1.34) 4,92 19064 1,4 YjlD BG13203 similar to NADH dehydrogenase 63,5 247,9 6,29 41794 1,5 Hag BG10655 flagellin 376,0 263,3 4,78 32472 1,6 FtsY BG11539 signal recognition particle (docking protein) 288,9 253,0 5,08 36187 1,6 SecA BG10741 preprotein translocase subunit (ATPase) 233,8 88,8 5,34 95334 1,7 DivIVa BG11835 cell-division initiation protein (septum placement) 4,85 19196 1,7 Gid BG11008 glucose- inhibited division protein 140,4 188,3 5,76 47899 1,8 Spo0M BG12229 disruption or overproduction has negative effects on 477,0 298,6 4,28 29557 sporulation; syn YgaI 1,8 SpoIVA BG10275 required for proper spore cortex formation and coat assembly; 414,7 161,4 4,55 55007 syn SpoVP 1,8 SpoVG BG10112 required for spore cortex synthesis 274,7 583,5 5,11 10755 2,1,1 AckA BG10813 acetate kinase (EC 2.7.2.1) 282,8 224,2 5,19 42976 2,1,1 AcoA BG12558 acetoin dehydrogenase E1 component (TPP-dependent alpha 338,8 249,0 4,91 35912 subunit); syn YfjK 2,1,1 AcoB BG12559 acetoin dehydrogenase E1 component (TPP-dependent beta 456,8 253,3 4,4 36689 subunit); syn YfjJ 2,1,1 AcsA-C1 BG10370 acetyl CoA synthetase (EC 6.2.1.1) 5,55 64717 2,1,1 AcsA-C2 BG10370 acetyl CoA synthetase (EC 6.2.1.1) 5,55 64717 2,1,1 GlpK BG10187 glycerol kinase (EC 2.7.1.30) 346,3 180,8 4,98 54910 2,1,1 IolC BG11119 similar to fructokinases, 2-keto-3-deoxygluconate kinases and 365,1 213,4 4,78 35476 ribokinases of bacteria 2,1,1 IolD BG11120 myo-inositol catabolism 285,2 112,3 5,01 63960 2,1,1 IolH BG11123 myoinositol catabolism 328,3 309,6 4,99 33370 2,1,1 IolI BG11124 similar to glyoxylate-induced protein of H. influenzae 410,3 332,6 4,66 31503 2,1,1 IolS BG11363 similar to auxin-induced protein of common tobacco, similar to 235,8 268,4 5,38 35014 oxidoreductases; syn YxbF 2,1,1 MalA BG11839 6-phospho alpha glucosidase (EC 3.2.1.122), syn GlvA 4,74 50384 30 Fermentation proteome profiling Antelmann et al. 2,1,1 MalL BG12421 oligo-1,4-1,6-alpha-glucosidase (sucrase-maltase-isomaltase) 338,7 149,2 4,98 65906 2,1,1 Pta BG10634 phosphate acetyltransferase (EC 2.3.1.8.) 415,7 283,7 4,65 34636 2,1,1 PtsH BG10200 phosphocarrier protein of phosphotransferase system 377,6 573,1 4,58 9051 2,1,1 RbsK BG10877 ribokinase (EC 2.7.1.15) 407,2 245,0 4,61 30986 2,1,1 YdjL BG12803 similar to L-iditol 2-dehydrogenase 358,9 213,5 4,8 37186 2,1,1 YhfE BG13051 similar to glucanase 131,6 213,2 5,88 38579 2,1,1 YjdE BG13177 similar to mannose-6-phosphate isomerase 260,0 236,9 5,27 35848 2,1,1 YqiQ BG11720 unknown; similar to phosphoenolpyruvate mutase 5.279 32942 2,1,1 YsdC BG12317 similar to endo-1,4-beta-glucanase 202,4 233,8 5,55 39059 2,1,1 YtoP BG13898 similar to endo-1,4-beta-glucanase 173,2 260,4 5,65 39079 2,1,1 YvcT BG12409 similar to glycerate dehydrogenase 306,8 291,3 5,09 36463 2,1,2 Eno BG10899 enolase (EC 4.2.1.11) 436,6 210,2 4,49 46418 2,1,2 FbaA BG10412 fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) 306,0 300,0 5,03 30248 2,1,2 GapA BG10827 glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) 298,9 236,6 5,03 35676 2,1,2 GapB BG12592 glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) 14,6 248,8 6,45 37320 2,1,2 PckA BG11841 phosphoenolpyruvate carboxykinase (EC 4.1.1.49) 295,1 155,5 5,11 58128 2,1,2 PdhA BG10207 pyruvate dehydrogenase (E1 alpha subunit) (EC 1.2.4.1) 114,6 241,0 5,84 41390 2,1,2 PdhB BG10208 pyruvate dehydrogenase (E1 beta subunit) (EC 1.2.4.1) 432,2 265,6 4,55 35320 2,1,2 PdhC BG10209 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase 357,9 151,6 4,86 47376 E2 subunit) (EC 2.3.1.12) 2,1,2 PdhD BG10210 dihydrolipoamide dehydrogenase E3 subunit of both pyruvate 373,8 157,4 4,76 49567 dehydrogenase and 2-oxoglutarate dehydrogenase complexes (EC 1.8.1.4) 2,1,2 Pfk BG12644 6-phosphofructokinase (EC 2.7.1.11) 62,5 280,4 6,14 34100 2,1,2 Pgi BG11720 glucose-6-phosphate isomerase 5.28 32942 2,1,2 Pgk BG11062 phosphoglycerate kinase (EC 2.7.2.3) 379,4 214,2 4,77 42030 2,1,2 Pgm BG10898 phosphoglycerate mutase (EC 5.4.2.1) 278,0 137,6 5,21 56140 2,1,2 PycA BG12660 pyruvate carboxylase (EC 6.4.1.1) 237,5 63,7 5,41 127721 2,1,2 Tkt BG11247 transketolase (EC 2.2.1.1) 361,7 108,6 4,8 72163 2,1,2 Tpi BG10897 triose phosphate isomerase (EC 5.3.1.1) 367,1 323,2 4,79 26880 2,1,2 YwjH BG10413 similar to transaldolase 180,8 407,4 5,61 19830 2,1,2 Zwf BG11739 unknown; similar to glucose-6-phosphate 1-dehydrogenase 5,28 55492 (pentose phosphate) 2,1,3 CitB BG10478 aconitate hydratase (EC 4.2.1.3) 333,1 69,5 4,9 99136 2,1,3 CitC BG10856 isocitrate dehydrogenase (EC 1.1.1.42) 373,0 221,9 4,83 46255 2,1,3 CitG BG10384 fumarate hydratase (EC 4.2.1.2) 209,9 199,1 5,47 50365 2,1,3 CitH BG11386 malate dehydrogenase (EC 1.1.1.37) 388,1 283,6 4,73 33490 2,1,3 CitZ BG10855 citrate synthase II (EC 4.1.3.7) 221,2 240,2 5,45 41569 2,1,3 OdhA BG10272 2-oxoglutarate dehydrogenase (E1 subunit) (EC 1.2.4.2) 205,2 73,8 5,84 105093 2,1,3 SdhA BG10352 succinate dehydrogenase (flavoprotein subunit) (EC 1.3.99.1) 204,3 134,9 5,71 65174 2,1,3 SucC BG12680 succinyl-CoA synthetase (beta subunit) ( EC 6.2.1.5) 357,8 237,7 4,85 41212 2,1,3 SucD BG12681 succinyl-CoA synthetase (alpha subunit) (EC 6.2.1.5) 181,0 304,8 5,59 31229 2,2 Ald BG10468 L-alanine dehydrogenase (EC 1.4.1.1) 281,2 212,6 5,12 39525 2,2 AnsB BG10301 L-aspartase (EC 4.3.1.1) 196,8 173,4 5,69 52386 2,2 ArgC BG10191 N-acetylglutamate gamma semialdehyde dehydrogenase (EC 295,1 248,9 5,17 37917 1.2.1.38) 2,2 ArgD BG10194 N-acetylornithine aminotransferase (EC 2.6.1.11) 87,2 246,8 5,93 40735 2,2 ArgF BG10197 ornithine carbamoyltransferase (EC 2.1.3.3) 320,6 224,0 4,96 34509 2,2 ArgG BG12570 argininosuccinate synthase (EC 6.3.4.5) 315,3 197,5 5,03 44657 2,2 AroA BG10375 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (EC 234,6 241,3 5,34 39382 4.1.2.15) and chorismate mutase (EC 5.4.99.5) 2,2 AroF BG10284 5-enolpyruvoylshikimate-3-phosphate phospholyase, 100,0 216,5 6,58 39812 chorismate synthase (EC 4.6.1.4) 2,2 Asd BG10783 aspartate semialdehyde dehydrogenase (EC 1.2.1.11) 320,3 216,2 4,97 37690 31 Fermentation proteome profiling Antelmann et al.