Supporting Information for Proteomics DOI 10.1002/pmic.200701017 Cao Xuan Hieu, Birgit Voigt, Dirk Albrecht, Drte Becher, Thierry Lombardot, Frank Oliver Glckner, Rudolf Amann, Michael Hecker and Thomas Schweder Detailed proteome analysis of growing cells of the planctomycete Rhodopirellula baltica ª 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com RB12697 NagA_3 CarB SecA_1 PolA RpoB GdhP ValS PutA RB6610 RB6127 PurL TolB_1 FusA_1 RB9034 RB12056 RB8067 RB641 RB12666 LeuS RB3424 RB10835 GyrB_3 AlaS RB7590 CitB RB452 Sps MutS PheT Dpp4RB6590 Sps SerC PpdK PpdK RB7538 ClpB RB1793 FusA_1 Pnp_2 ClpC PpdK RB404RB24 RB4703 Pnp_2 RB12337RB1950 FusA_2 RB973 RpsA_2 DnaK_4 RB9674Icd ThrS RB2160RB3405RB2367 RB10709TypA RB3842 RB2860 AcsA Tkt RB4561 Tig Dnak_2 RB4703RB8337 RB8843 MdoG Prc SdhA ArgS CysN RB512 DegP_4 RB9029 RB10078 RB10027 RB8745 NusA GlgB_2 Ask PmmRB9674AspS_4RB1002RpsA_1 RB6127 RB12968RB8674 Pmm GroEL_3 RB5140 RB1252 MetX RB1722 IlvD_2 GlgB_1 Ogt_3RB7190 RB6491 AceF GroEL_2 XylA Dxs MalQ RB5608 LysS PolB GpmI 6pgD RB9992 RB12905 PyrG RB9110 TypA PhoA GlyS RB6395 GabD RB5608 GuaA_2GroEL_1RB6416HtrA_1 RB8375PhoA RB9438 RB10180 SerA_2 RB12905 PilB_2 UxuB RB9029 PurH CysSCysS HemD AslA_4 GlgB_2GabD RB1523 GatB UgdH RB307PyrC_1RB2261 RB1854 AslA_4 RB1634 RB9995 GroEL_2TrpE DldH RB2254 GabD NtrC_3 RB1359 KatA RB5 RB6888 GatAGatARB5786 HisD RB9262 LeuA_2PykA RB3710NadB ArsA_9 ArsA_9 RB12461 PepT_1 RB10048 SerSRB11174 GltD GcvPB ArsA_9 SthA SthA RB11998 RB6486Pnp_2 FumC PurDAdk_1 RB8557 RB1359 RB2732 HisS GltXYqhJ ProS GlyA RB10127 NtrC_3 PepA HsdM_1 Hom AsnS ChlI NqrA RB538 RB11879 RB6977 RB8941 RB683 PgiTrkALpd RB45276pgDRB1533ThiC RB3070 AtoC_1 G6pD RB5697 RB4654 RB10127 RpoA_2 RB1579 PurB ArsA_9 RB1308 RB9402 DapE ProA EutE AccC LeuC ArsA_9 ArsA_9 RB5763 RB1359 MetKAtpA_1 AtpB_2 XylA SerC RB4582 GlyA RB1939 RB12882 RB8228 BcpC LysA_3 AhcY RB9196PfkA ThrC RB9404 RpoA_2 Pgk RB9832SerA_1 RibA RB9527 RB7598 RB4129 PrfB FabF_2 RB1555 RB9527 FixW RB12541 ScrK RB520 GltA PurB LeuC RB2630 RB9971 RB6985 RB6384RB11150 RB5186 RB1535Fdh_1 RB85 CarA TrpB RB11502 RB9971 RB4256 Eno AspC_2 Pfk RB1939TufA GlgC_1 AlgU DnaN_5 SucC MexA RB8221 GdhA MoxR_4 RB7364 TyrS FabF_3 RB6199 YacI RB8799 RB9026 RB9030 RB10061 GalM_2 MoxR_3 ManC Gcd HemL Fdh_2 RB7610 RB8221 RB10503 RB10061 HtrA_2 Trx_3RB5223 PrfA RB9261 RB9132 RB3597 RB4182 RB3330RB457 PilT_1 Tal LeuB_1 SucC Ald MoxR_9 RB10503 GcvT NqrC Tal GlnIIRB2640 CelM RB2822 RB12038 RB2782 Fmt FbaB SphX SucC KdgK AroA YjjN Tas TsfRB10124 RB3686 RB1743 PilT_2 RB3221 RB12035 Adh_3 RpoA_1 RB2518 RB8870RB7193 RB3476 RB3924 RB4399 RB4742 MoxR_8 GalE_2 KdgK PyrD_1 RB1260 RB12361 RB7785 YeaC UspA_2MoxR_10 GapA RB4759 AtpG_1 RB3733 KorB RB10652 PurC HemKRB2901 AspC_3 AspC_1 GalE_1 YbhE FbaB RB2912 PheS FbaRB8768 RB9584 GapA AroG AroG DapB RB8328 RB4744 GalM_1 IolI RB11008RB1088 RB6236 RB6603 RB12347 RB2498 RB9512 GlnII RB6236 IlvC SucDRB203 RB6771 RB12556 PyrB_2 RB10028 RB4654 DapA_1 RB6799 ThiL RB4432 RB6658 RB2501 TrpS Fpr HpnA RB11985 CheY_1RB11262 AtpG_1 CysK MraW RB12489 RB4404 Ldh_2 RB4041 RB5404 RB10287 RB4404 RB279RB8266 RB6858 AccA Gnl_2 RB10727 RB9037 AroG RB9998 GlmURB6386 RB5811 RB1248 RB2521 RB5500FabDRB10478 RB1248 ExoA GlcK_1RB1483 RB7120 GlmU LolI RB1321 RB2568 RB9518 Fba RB11728 KpsU RB7166 RB8677 RB1109 RB3632RB9945 RB1411 RB3694 RB6145RB11575 RB8846 RB5042RB3689 IlvE_2 RB12844RB321 UspA_1 RB1412 RB12844 RB2714 Gdh RB3239 SgaU MetF IlvE_2 MurBRB1044RB6530 RB10088 FabI_1 RB11010 RB10195 RB11494 HpaG RB5352 RB12167 PfaS RB13257 RB8957 RB4532 RB8783 ProC Psd_1 RB2656 RplY PyrF PtsN RB8246 PanB RB8202 RB2647 Efp_2 RB12073 RB6403 RB12372 RB1939 PhoU RB6430 DltE NusG Rpe Mip_1 RB6430 RB6469 RB4394RB10907 Pgl Pa1G RB8246 RB201 RB6403 RB2242 RibE TpiA RB6430 RB4127 RB9849 RB8163 RB10789 RB4464 RB4464 RB5031 MsrA_1 RB7235 RB6615LolD1 RB11030 RspB RuvA RB7235RB11946 RB9218 HisB GrpE Efp_1 HisH PhoB RB4866 Def RB2680 RB12301 RB569 LeuD Frr RB11516 RB11107 RB12301 RB569PyrE SodA PrdX2 Apt PyrE RB11107 RB2125 RB6586 RB2743 PrdX2 ClpP_1 AtpD_1 RB7658 RB3471 GreA RB12060 RpsP RplI CpaB ClpP_2 TPX RB7822 RB4395 FabZ_1 TPX FabZ_1 RB10483 RB4405 RB12297 Ndk RB6941 Ssb RB6792 IlvN RB9101 RplL RB4468 RB7203 RB5240 RB10530 RB9101 CypH RB9101 RB5749 Bfr PpiB RB9190 RB8067 RB4433 RB4438 RplJ RB6217 RB4347 Hsp20_2 RB4347 FruA RB1270 RbfA RB11176 RB8559 RB8067 GroES_1 RpoZ RB10956 RpsF TrxA_2 RB6217 RB1753 DksA_1 RB8520 AtpE_2 RB12634 RB6428 RB34 RB8580 RplU GroES_2 Grp GroES_2 RB4474 GlnB_2 RB5657 RB4480 RB10934 RpmC Supplementary Figure 1 Supplementary Figure 1. The R. baltica master gel. Proteins from cells in the exponential growth phase were separated in a pH 4-7 gradient. The gel was stained with colloidal Coomassie Brilliant Blue. 1 Supplementary Table 1. List of all identified proteins of R. baltica. COG, Clusters of Orthologous Groups of proteins were estimated on the NCBI database (A, RNA processing and modification; B, Chromatin structure and dynamics; C Energy production and conversion; D, Cell cycle control, mitosis and meiosis; E, Amino acid transport and metabolism; F, Nucleotide transport and metabolism; G, Carbohydrate transport and metabolism; H, Coenzyme transport and metabolism; I, Lipid transport and metabolism; J, Translation; K, Transcription; L, Replication, recombination and repair; M, Cell wall/membrane biogenesis; N, Cell motility; O, Posttranslational modification, protein turnover, chaperones; P, Inorganic ion transport and metabolism; Q, Secondary metabolites biosynthesis, transport and catabolism; R, General function prediction only; S, Function unknown; T, Signal transduction mechanisms; U, Intracellular trafficking and secretion; V, Defense mechanisms; ++, not in COGs). Psortb, Predicted protein localization was obtained from PSORTb v.2.0 Precomputed Genome (http://www.psort.org/genomes/genomes.pl). New, proteins not identified in earlier proteome studies. 1-D, 2-D and nHPLC, indicate the protein/ peptide separation method used for intracellular proteins (1-D SDS PAGE combined with nHPLC, 2-D gel electrophoresis or nHPLC). Cell wall, proteins identified in cell wall associated fractions. Extracell, secreted proteins. SP scores, signal peptide scores derived from the SignalP 3.0 server. PHX, the predicted highly expression level based on codon usage optimization described by Karlin et al. [20]. Accession Protein Function pI Mr COG Psortb SP PHX New 1D 2D HPLC Cell Extracell Number name Score Gel Gel wall 1 Intermediary metabolism 1.1 C-compound and Carbohydrate metabolism 1.1.1 Glycolysis and Phosphogluconate pathways RB1629 GlcK_1 Glucokinase (EC 2.7.1.2) 5.56 38.0 K Cytoplasmic + + RB399 Pgi Glucose-6-phosphate isomerase (EC 5.3.1.9) 5.72 57.1 G Cytoplasmic + + (Synonyms: Gpi, Pgi, Phi) RB10591 Pfk PPi-phosphofructokinase (EC 2.7.1.90) 5.25 49.3 G Unknown + + + RB7572 PfkA 6-phosphofructokinase, pyrophosphate-dependent 6.20 51.8 G Cytoplasmic + + + (EC 2.7.1.11) RB6690 Fba Fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) 4.69 36.7 G Cytoplasmic + + + + RB4737 FbaB Fructose-bisphosphate aldolase class I (EC 6.70 40.1 G Cytoplasmic + + 4.1.2.13) RB7095 TpiA Triosephosphate isomerase (EC 5.3.1.1) (TIM) 4.54 26.6 G Cytoplasmic + + + + + RB2627 GapA Glyceraldehyde 3-phosphate dehydrogenase (EC 5.64 36.7 G Cytoplasmic + + + + + + 1.2.1.12) RB10500 Pgk Phosphoglycerate kinase (EC 2.7.2.3) 4.72 41.3 G Cytoplasmic + + + + RB8562 GpmI 2,3-bisphosphoglycerate-independent 4.96 59.0 G Cytoplasmic + phosphoglycerate mutase (EC 5.4.2.1) (iPGM) RB12381 Eno Enolase (EC 4.2.1.11) 4.43 45.9 G Cytoplasmic + + + + RB10277 PykA Pyruvate kinase (EC 2.7.1.40) 5.24 52.2 G Cytoplasmic + + RB2735 G6pD Glucose-6-phosphate 1-dehydrogenase (EC 6.30 55.1 G Cytoplasmic + + + 1.1.1.49) (G6PD) RB9089 Pgl 6-phosphogluconolactonase (EC 3.1.1.31) 4.75 26.0 G Unknown + + RB2817 Gnd 6-phosphogluconate dehydrogenase, 5.08 54.0 G Cytoplasmic + + + + + decarboxylating (EC 1.1.1.44) RB1561 Rpe Ribulose-phosphate 3-epimerase (EC 5.1.3.1) 4.36 25.1 G Cytoplasmic + + + RB12921 Tkt Transketolase (EC 2.2.1.1) 4.99 73.4 G Unknown + + + + RB3193 Tal Transaldolase (EC 2.2.1.2) 4.56 41.4 G Cytoplasmic + + + + RB1819 GalE_1 Udp-glucose 4-epimerase (EC 5.1.3.2) 5.23 36.7 M Unknown + RB2884 GalE_2 Probable UDP-glucose epimerase (EC 5.1.3.2) 5.08 40.4 M Cytoplasmic + + RB1220 GalM_1 Probable aldose 1-epimerase (EC 5.1.3.3) 6.25 39.5 G Multipe + + localization sites RB6537 GalM_2 Aldose 1-epimerase (EC 5.1.3.3) 4.71 42.2 G Periplasmic 0.99 + + + RB3751 UDP-glucose 4-epimerase homolog (EC 5.1.3.2) 5.68 40.8 M Unknown + RB1784 UgdH UDP-glucose 6-dehydrogenase (EC 1.1.1.22) 4.67 52.3 M Unknown + RB5197 Sps Sucrose-phosphate synthase 1 (EC 2.4.1.14) 5.13 86.9 M Cytoplasmic + + + RB10002 Gcd Glucose dehydrogenase Gcd 4.88 40.7 E Cytoplasmic + + RB5577 Gnl_1 Gluconolactonase (EC 3.1.1.17) 5.14 39.6 G Unknown 0.79 + + RB12740 Gnl_2 Gluconolactonase (EC 3.1.1.17) 4.86 43.3 G Unknown + RB7294 Gdh Probable glucose 1-dehydrogenase (EC 1.1.1.47) 5.98 30.4 Q Cytoplasmic + RB683 Aldehyde dehydrogenase (EC 1.2.1.3) 4.80 52.5 C Cytoplasmic + + + + RB8941 Ketoglutarate semialdehyde dehydrogenase (EC 4.65 58.0 C Cytoplasmic + + 1.2.1.3) RB10172 Aldehyde dehydrogenase (EC 1.2.1.3) 5.05 53.4 C Cytoplasmic + + RB8731 KdgK 2-keto-3-deoxygluconate kinase (EC 2.7.1.45) 5.15 39.4 G Unknown + + + RB1998 PpdK Pyruvate,phosphate dikinase (EC 2.7.9.1) 6.10 97.0 G Cytoplasmic + + + + + + + RB6729 DeoC Deoxyribose-phosphate aldolase (EC 4.1.2.4) 5.34 27.9 F Cytoplasmic + + (Phosphodeoxyriboaldolase) (Deoxyriboaldolase) (DERA) RB4944