Supporting Information for Proteomics DOI 10.1002/pmic.200600859
Daniela Fojo Seixas Chaves, P rcio Pereira Ferrer, Emanuel Maltempi de Souza, Leonardo Magalh es Gruz, Rose Adele Monteiro and F bio de Oliveira Pedrosa
A two-dimensional proteome reference map of Herbaspirillum seropedicae proteins
ยช 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Supplementary Table 1. Complete list of H. seropedicae identified proteins.
Spot Accession IDa Numberb Protein name
1 CAM32534.1 Chaperone protein dnaK (HSP70)
2 CAM32674.1 Polyribonucleotide nucleotidyltransferase
3 CAM32559.1 Elongation factor G 1 (EF-G 1)
4 CAM32640.1 ATP-dependent Clp protease subunit (heat-shock)
5 CAM32585.1 30s ribosomal subunit protein S1
6 CAM32629.1 Dihydrolipoamide dehydrogenase
7 CAM32626.1 Catalase (peroxidase I)
8 CAM32583.1 NADP-dependent malic enzyme oxidoreductase
9 CAM32583.1 NADP-dependent malic enzyme oxidoreductase
10 CAM32547.1 NADH dehydrogenase I (Chain G) oxidoreductase
12 CAM32545.1 CTP synthase (UTP-ammonia lyase)
13 CAM32579.1 Phosphoenolpyruvate carboxykinase
14 CAM32603.1 Glutamine synthetase
15 CAM32607.1 Glutamine synthetase
16 CAM32690.1 Chaperonin GroEL (HSP60 family)
17 CAM32690.1 Chaperonin GroEL (HSP60 family)
18 CAM32550.1 Peptidyl-prolyl cis/trans isomerase (trigger factor)
19 CAM32670.1 F0F1-type ATP synthase, beta subunit
20 CAM32680.1 Histidinol dehydrogenase oxidoreductase
21 CAM32659.1 XAA-PRO aminopeptidase
22 CAM32670.1 F0F1-type ATP synthase, beta subunit
23 CAM32546.1 Enolase
24 CAM32546.1 Enolase
25 CAM32610.1 Succinyl-CoA synthetase protein, beta chain
26 CAM32610.1 Succinyl-CoA synthetase protein, beta chain
26 CAM32569.1 Thioredoxin reductase oxidoreductase
28 CAM32678.1 SAM-dependent methyltransferase
29 CAM32556.1 Conserved hypothetical protein
30 CAM32651.1 Sugar kinase ribokinase family
31 CAM32688.1 NADPH:quinone oxidoreductase
32 CAM32688.1 NADPH:quinone oxidoreductase
33 CAM32668.1 Probable DNA-directed RNA polymerase (alpha chain)
34 CAM32665.1 Actin-like ATPase involved in cell morphogenesis
35 CAM32604.1 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
37 CAM32549.1 FKBP-type peptidyl-prolyl cis-trans isomerase (Rotamase)
38 CAM32575.1 Elongation factor TS (EF-TS)
40 CAM32595.1 Xanthine dehydrogenase (subunit A)
40 CAM32643.1 3-isopropylmalate dehydrogenase oxidoreductase
40 CAM32571.1 Flagellin protein; filament structural
41 CAM32590.1 GTPase translation elongation factor TU (EF-Tu)
42 CAM32557.1 S-adenosylmethionine synthetase
43 CAM32667.1 Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex
44 CAM32631.1 Argininosuccinate synthase
46 CAM32540.1 Seryl-tRNA synthetase
47 CAM32660.1 Parvulin-like peptidyl-prolyl cis-trans isomerase
48 CAM32536.1 Phosphoribosylaminoimidazolecarboxamide formyltransferase and IMP cyclohydrolase transmembrane
48 CAM32648.1 Fumarate hydratase
49 CAM32535.1 Electron transfer flavoprotein-ubiquinone oxidoreductase
50 CAM32677.1 F0F1-type ATP synthase, alpha subunit
52 CAM32562.1 Glutamate synthase (small subunit) oxidoreductase
53 CAM32573.1 2-oxoglutarate dehydrogenase, E3 component, lipoamide dehydrogenase
54 CAM32592.1 Adenylosuccinate synthetase
55 CAM32650.1 Biotin carboxylase
56 CAM32565.1 Tartrate dehydrogenase
57 CAM32635.1 Glutamate-1-semialdhyde 2,1-aminomutase
58 CAM32565.1 Tartrate dehydrogenase
59 CAM32688.1 NADPH:quinone oxidoreductase
60 CAM32623.1 Galactose-1-phosphate uridylyltransferase
61 CAM32601.1 Sulfate adenylyltransferase subunit 2
62 CAM32612.1 Fructose-1,6-bisphosphate aldolase
63 CAM32598.1 Acetylornithine aminotransferase
65 CAM32553.1 HlyD family membrane-fusion
66 CAM32644.1 Acetyl-CoA acyltransferase
67 CAM32632.1 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
68 CAM32581.1 ABC-type proline/glycine betaine transport system, ATPase component
68 CAM32622.1 UDP-N-acetylglucosamine 2-epimerase
69 CAM32621.1 Aryl-alcohol dehydrogenase
70 CAM32560.1 Phosphoribosylpyrophosphate synthetase
71 CAM32686.1 Fructose-1,6-bisphosphatase
72 CAM32701.1 Malate dehydrogenase
73 CAM32630.1 L-asparaginase/archaeal Glu-tRNAGln amidotransferase subunit D
74 CAM32621.1 Aryl-alcohol dehydrogenase
75 CAM32701.1 Malate dehydrogenase
76 CAM32621.1 Aryl-alcohol dehydrogenase
77 CAM32621.1 Aryl-alcohol dehydrogenase
78 CAM32645.1 Acetyl-CoA acetyltransferase (acetoacetyl-CoA thiolase)
79 CAM32645.1 Acetyl-CoA acetyltransferase (acetoacetyl-CoA thiolase)
80 CAM32599.1 Septum site-determining
81 CAM32613.1 Phosphoribosylaminoimidazole-succinocarboxamide synthase
82 CAM32542.1 Inositol monophosphatase (extragenic suppressor)
83 CAM32663.1 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase
84 CAM32654.1 Sugar phosphate isomerase (involved in capsule formation)
85 CAM32552.1 Pantoate-beta-alanine ligase (panthothenate synthetase)
86 CAM32663.1 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase
88 CAM32611.1 Succinyl-CoA synthetase alpha chain
90 CAM32611.1 Succinyl-CoA synthetase alpha chain
91 CAM32558.1 Acetylglutamate kinase
92 CAM32694.1 Probable universal stress proten
93 CAM32694.1 Probable universal stress protein
94 CAM32703.1 Succinate dehydrogenase Fe-S protein subunit protein
95 CAM32565.1 Tartrate dehydrogenase
95 CAM32597.1 ATPase with chaperone activity, ATP-binding subunit
96 CAM32629.1 Dihydrolipoamide dehydrogenase (E3 component of pyruvate and 2- oxoglutarate dehydrogenases complexes)
Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide 97 CAM32648.1 isomerase
98 CAM32661.1 Acyl CoA:acetate/3-ketoacid CoA transferase, beta subunit protein
ABC-type proline/glycine betaine transport system, periplasmic component 99 CAM32580.1
100 CAM32683.1 Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF- 5A)
102 CAM32616.1 Heat shock protein 24 (HSP-70 cofactor)
103 CAM32591.1 Inorganic pyrophosphatase
105 CAM32682.1 Transmembrane ubiquinol-cytochrome C reductase (Iron-sulfur subunit) oxidoreductase
106 CAM32624.1 Hypothetical protein
107 CAM32618.1 Dihydrodipicolinate reductase
CAM32657.1 Conserved hypothetical protein; Predicted periplasmic or secreted 108 lipoprotein
109 CAM32602.1 Carboxyphosphonoenolpyruvate phosphonomutase
110 CAM32619.1 Protein-L-isoaspartate O-methyltransferase
111 CAM32614.1 Pyridoxamine 5`-phosphate oxidase
112 CAM32664.1 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
113 CAM32539.1 Peroxiredoxin
114 CAM32661.1 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit
117 CAM32605.1 Adenylate kinase (ATP-AMP transphosphorylase)
118 CAM32698.1 Acetoacetyl-CoA reductase
120 CAM32564.1 Phasin family protein
125 CAM32538.1 Probable ABC-type glutamate/aspartate transport system, ATPase component
126 CAM32539.1 Peroxiredoxin
128 CAM32688.1 NADPH:quinone oxidoreductase
129 CAM32606.1 Superoxide dismutase [Fe]
130 CAM32698.1 Acetoacetyl-CoA reductase
131 CAM32673.1 Methyl-accepting chemotaxis
137 CAM32551.1 ATP-dependent Clp protease (proteolytic subunit)
140 CAM32544.1 Transcription elongation factor
142 CAM32671.1 F0F1-type ATP synthase, epsilon subunit (mitochondrial delta subunit)
143 CAM32669.1 DnaK suppressor
145 CAM32554.1 Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family
146 CAM32702.1 Polybetahydroxybutyrate accumulation regulatory (PhbF)
148 CAM32600.1 Conserved hypothetical protein
149 CAM32615.1 Signal peptide
151 CAM32653.1 Single-strand DNA-binding protein (helix-destabilizing protein)
153 CAM32574.1 Transmembrane protein
155 CAM32639.1 S-adenosylmethionine:2-demethylmenaquinone methyltransferase
157 CAM32596.1 FOG: CBS domain containing
158 CAM32609.1 FKBP-type peptidyl-prolyl cis-trans isomerase I
160 CAM32593.1 Conserved hypothetical protein
162 CAM32543.1 Glycolate/propanediol utilization
163 CAM32689.1 Co-chaperonin GroES (HSP10)
164 CAM32572.1 Nucleoside-diphosphate kinase
165 CAM32578.1 Universal stress protein
166 CAM32567.1 Nitrogen regulatory P-II protein
168 CAM32693.1 Conserved hypothetical protein
171 CAM32617.1 Ferric uptake regulator
174 CAM32548.1 Conserved hypothetical protein
176 CAM32652.1 Probable exported protein
178 CAM32655.1 Hypothetical protein
Phosphopantetheine adenylyltransferase 179 CAM32676.1
180 CAM32679.1 UDP-N-acetylglucosamine pyrophosphorylase
181 CAM32675.1 Zinc protease-like signal peptide
182 CAM32581.1 ABC-type proline/glycine betaine transport system, ATPase component
183 CAM32612.1 Fructose-1,6-bisphosphate aldolase
184 CAM32697.1 Beta-hydroxybutyrate dehydrogenase
189 CAM32570.1 PKHD-type hydroxylase
190 CAM32555.1 Acetyl-coenzyme A carboxylase carboxyl transferase (alpha subunit)
191 CAM32611.1 Succinyl-CoA synthetase alpha chain
192 CAM32537.1 Conserved hypothetical protein
192 CAM32566.1 Probable ubiquinone biosynthesis protein COQ7
194 CAM32590.1 GTPase translation elongation factor TU (EF-Tu)
195 CAM32628.1 Probable HSP90 family high temperature molecular chaperone G
196 CAM32633.1 Glyceraldehyde 3-phosphate/erythrose-4-phosphate dehydrogenase
197 CAM32563.1 Electron transfer flavoprotein, alpha subunit
198 CAM32594.1 Aspartate-semialdehyde dehydrogenase
199 CAM32541.1 Hydrolase or acyltransferase
200 CAM32614.1 Pyridoxamine 5`-phosphate oxidase
201 CAM32587.1 GMP synthase
202 CAM32646.1 DNA-binding ferritin-like protein (oxidative damage protectant)
205 CAM32577.1 UTP-glucose-1-phosphate uridylyltransferase
206 CAM32582.1 TetR-family transcriptional regulator
207 CAM32647.1 Thiamine monophosphate synthase
209 CAM32685.1 Conserved hypothetical protein
211 CAM32625.1 Imidazoleglycerol-phosphate synthase
213 CAM32568.1 NAD+ dependent acetaldehyde dehydrogenase
214 CAM32539.1 Peroxiredoxin
215 CAM32576.1 30S ribosomal subunit protein S2
217 CAM32687.1 Hypothetical protein
218 CAM32584.1 Signal peptide
219 CAM32589.1 30S ribosomal subunit protein S10
221 CAM32642.1 30S ribosomal subunit protein S6
222 CAM32641.1 50S ribosomal subunit protein L9
223 CAM32588.1 Intracellular protease/amidase
224 CAM32692.1 VGR-related protein
226 CAM32684.1 Sulfurtransferase (Rhodanese-like)
227 CAM32606.1 Superoxide dismutase [Fe]
228 CAM32561.1 50S ribosomal subunit protein L25
229 CAM32585.1 30s ribosomal subunit protein S1
230 CAM32688.1 NADPH:quinone oxidoreductase
231 CAM32674.1 Polyribonucleotide nucleotidyltransferase
232 CAM32674.1 Polyribonucleotide nucleotidyltransferase
233 CAM32671.1 FOF1-type ATP synthase, delta subunit
234 CAM32695.1 Conserved hypothetical protein
235 CAM32666.1 Co/Zn/Cd efflux system component
236 CAM32637.1 TRNA nucleotidyltransferase (ribonuclease PH)
237 CAM32656.1 Signal peptidase I family protein
238 CAM32672.1 Homoserine kinase
239 CAM32634.1 N-acetyl-gamma-glutamyl-phosphate reductase
240 CAM32699.1 50S ribosomal subunit protein L6/L9E
241 CAM32586.1 N-acetylglucosaminyltransferase
242 CAM32600.1 Conserved hypothetical protein
243 CAM32560.1 Phosphoribosylpyrophosphate synthetase
244 CAM32620.1 UDP-glucose 4-epimerase
245 CAM32636.1 Ketol-acid reductoisomerase oxidoreductase
246 CAM32608.1 Dehydrogenase oxidoreductase protein
247 CAM34548.1 Conserved hypothetical protein; probably Ser protein
248 CAM34549.1 Conserved hypothetical protein
249 CAM32644.1 Acetyl-CoA acyltransferase
250 CAM32658.1 DNA gyrase subunit B, type II topoisomerase, ATPase activity
251 CAM32565.1 Tartrate dehydrogenase
252 CAM35232.1 Probable conserved hypothetical protein
253 CAM35233.1 Conserved hypothetical protein
a) Spot ID in the 2D gel; b) Protein identifier in the EMBL protein database (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=protein). Supplementary Table 2. KEGG pathways represented by more than 3 enzymes.
Pathway Number of enzymes Purine metabolism 11 Glycolysis/gluconeogenesis 10 Pyruvate metabolism 10 Citrate cycle 7 Butanoate metabolism 7 Oxidative phosphorylation 5 Propanoate metabolism 5 Fatty acid metabolism 4 Pyrimidine metabolism 4 Valine, leucine and isoleucine degradation 4 Urea cycle and metabolism of amino groups 4 Glycine, serine and threonine metabolism 3 Pentose phosphate pathway 3 Galactose metabolism 3 Synthesis and degradation of ketone bodies 3 Glutamate metabolism 3 Alanine and aspartate metabolism 3 Lysine biosynthesis 3 Lysine degradation 3 Histidine metabolism 3 Tryptophan metabolism 3 Nucleotide sugars metabolism 3 Glycerolipid metabolism 3 Pantothenate and CoA biosynthesis 3 Nitrogen metabolism 3
1
Supplementary Table 3. Proteins identified in multiple spots in the 2D electrophoresis gel of H. seropedicae.
Protein Accession Isoformsb numbera 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase CAM32663.1 2 (c) 30s ribosomal subunit protein S1 CAM32585.1 2 (c) ABC-type proline/glycine betaine transport system, ATPase component CAM32581.1 2 (c) Acetoacetyl-CoA reductase CAM32698.1 2 (c) Acetyl-CoA acetyltransferase CAM32645.1 2 (c) Aryl-alcohol dehydrogenase CAM32621.1 4 (c) Chaperonin GroEL (HSP60 family) CAM32690.1 2 (c) Dihydrolipoamide dehydrogenase CAM32557.1 2 (c) Enolase CAM32546.1 2 (c) F0F1-type ATP synthase, beta subunit CAM32670.1 2 (c) Fructose-1,6-bisphosphate aldolase CAM32612.1 2 (c) Glutamine synthetase CAM32603.1 2 (c) GTPase translation elongation factor TU (EF-Tu) CAM32590.1 2 (c) Malate dehydrogenase CAM32701.1 2 (c) NADPH:quinone oxidoreductase CAM32688.1 5 (c, m) Peroxiredoxin CAM32539.1 2 (m) Phosphoribosylpyrophosphate synthetase CAM32560.1 2 (c,m) Polyribonucleotide nucleotidyltransferase CAM32674.1 3 (c) Pyridoxamine 5`-phosphate oxidase CAM32614.1 2 (c) Succinyl-CoA synthetase alpha chain CAM32611.1 3 (c) Succinyl-CoA synthetase protein, beta chain CAM32610.1 2 (c) Superoxide dismutase [Fe] CAM32606.1 2 (c, m) Tartrate dehydrogenase CAM32565.1 4 (c, m) Universal stress protein CAM32694.1 2 (c) a) Protein identifier in the EMBL protein database (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=protein); b) c: charge isoform; m: mass isoform