Table 1.
Expression profiling of bacterial strains in differential medias/plant associated bacteria as pathogens, symbiotic or epiphytes.
| Organism | Pathogen | Proteomic techniques | No. of IP1 | Virulence factor, secretion systems, proteins expressed in vivo or under defined medias in different bacteria | References |
|---|---|---|---|---|---|
| Xanthomonas campestris pv. Campestris/parasite | Brassica oleracea, (cv. Coracao de boi) 4–6 days after inoculation (DAI) | 2-DE, MALDI-TOF/TOF | 21 | Proteins from young leaves of susceptible Brassica cv infiltrated with X. campestris: aspartate semialdehyde dehydrogenase, elongation factor thermo unstable, phosphomannose isomerase, adenine triphosphate (ATP) synthase, ribosomal protein, chaperonin, phosphoglycerate kinase, and ATPase. | Andrade et al., 2008 |
| Frankia sp. Strains M16467/symbiont | Morella cerifera and Myrica gale | 2-DE, MALDI-TOF MS | 50 | With and without M. cerifera, M. gale seed phenolic extracts. Twenty proteins with increased abundance: signal transduction mechanisms, translation, ribosomal structure and biogenesis, chaperone heat shock protein, translation, amino acid and lipid transport, and metabolism. Thirty proteins with decreased abundance: Post-translational modification, chaperones, replication, transcription, translation, recombination, repair, energy production, conversion, lipid, inorganic ion, coenzyme, nucleotide, carbohydrate and secondary metabolite (transport and metabolism), cell wall biogenesis, and defense. | Bagnarol et al., 2007 |
| Pseudomonas savastanoi pv. savastanoi/6 weeks after infection | Olea europaea subsp. europaea cvs Galega and Cordovil de Serpa | 2-DE, MALDI-TOF MS | 7 | Proteins accumulated in vivo in O. europaea stems after infection by P. savastanoi: aconitate hydratase, tellurium resistance protein, enolase, hypothetical protein, and calcium dependent protein kinase. | Campos et al., 2009 |
| X. campestris pv. campestris strain | X. campestris pv. campestris strain 11A/17 | 2-DE, MALDI-TOD MS | 281 | General protein accumulation in X. campestris: energy, metabolism, carbohydrate, lipid, protein and cofactors and vitamins metabolism, biosynthesis of secondary metabolites, transcription, translation, replication and repair, membrane transport, signal transduction, cell motility (22 higly abundant proteins of virulent vs. avirulent: aspartate semialdehyde dehydrogenase, cold shock protein, elongation factor, cellulase, L-isoaspartate protein carboxyl methyltransferase, malate dehydrogenase, 50S ribosomal protein, fumaryl acetoacetate hydrolase, peptidyl-prolyl cis-trans isomerase, 10 kDa chaperonin). | Chung et al., 2007 |
| Bradyrhizobium Japonicum/Symbiont | Glycine max/21 DAI | LCMS/MS, LTQ-Orbitrap MS | 3587 genes/proteins | Proteins involved in translation, post transcriptional regulation, nitrogenase complex, aspartate amino transferase, carbon metabolism, translation, and nucleic acid metabolism. | Delmotte et al., 2010 |
| S. scabies | Wild type/tatC mutant strains | 2-DE, MALDI-TOF TOF MS | 73 | Tat dep virulence (vir) factors: glycosyl hydrolase domain, putative alpha-L-fucosidase, ABC-type Fe3+ transport system, periplasmic component, glycosyl hydrolase domain, hydrolase of the α/β superfamily, lipoprotein, spermidine/putrescine transporter peptide- binding protein, and rhamnosidase. | Joshi et al., 2010 |
| Sinorhizobium meliloti/Symbiont | Medicago truncatula and Melilotus alba | 2-DE, MALDI-TOF MS | 420/700 | Proteomes of the nodule bacteria compared to S. meliloti in vitro: transport proteins (ABC transporters, leucine and Iron binding protein), vitamin synthesis, stress-related processes, superoxide dismutase, betaine aldehyde dehydrogenase, heat shock protein, energy, GTP-binding proteins, oxidoreductase NAD protein, catalase, cell division, ribosomal protein, deoxyribonucleic acid transcription, translation, and central metabolism. | Djordjevic, 2004 |
| Methylobacterium extorquens/epiphyte | A. thaliana | 2-DE, LC MS/MS | 45 | PhytR regulated proteins: alcohol dehydrogenase, catalase, reactive oxygen species, stress proteins, lactoylglutathione lyase, dioxygenase, glutathione-dependent formaldehyde dehydrogenase, malyl lyase, malate dehydrogenase, glutathione-dependent formaldehyde dehydrogenase, haloacetate dehalogenase, transcription elongation factor, lipid metabolism, propionyl-CoA carboxylase, and dehydrogenases reductases. | Gourion et al., 2006 |
| Rhizobium. R. leguminosarum bv. trifolii strain ANU843/symbiont | flavonoid 7,4 dihydroxyflavone (released due to legume nodulation) | 2-DE, Protein sequencer | 12 | R. leguminosarum grown in presence and absence of 7,4-dihydroxyflavone: amino acid metabolism and transport, flagellin, protein translation and structure, energy, DnaK, NodE, and NodB. | Guerreiro et al., 1997 |
| Azoarcus sp. strain BH72/endophyte | PilR mutant (necessary for endophytic growth) | 2-DE, MALDI-TOF MS/MS, LC-MS/MS | 785/30 abundant | PilR mutant proteins: amino acid and energy metabolism, chaperones, iron metabolism and storage, ATP synthase, ABC transporter, heat shock protein, pyridoxal phosphate, DNA, RNA polymerase, S-adenosyl-L-homocysteine hydrolase, fumarate hydratase, and ATP-dependent protease. | Hauberg et al., 2010 |
| Burkholderia glumae (grain and seedling rot in rice, bacterial wilt in many crops) | Under hrpB expression (induced after attack to plant) | 2-DE, ESI-MS/MS | 34 secretory/12 cytoplasmic | Induction of type III secretion system (T3SS), acetylglutamate kinase, ribosomal protein, transcription elongation factor, Acetyl-CoA biotin carboxyl carrier protein, chaperone protein DnaK, lipoprotein, ATP synthase, phenylalanyl-tRNA synthase, and alkyl hydroperoxide reductase. | Kang et al., 2008 |
| Rhizobium leguminosarum Biovar viciae (symbiont) | Pisum sativum and Vicia cracca | Microarray | Genes expressed related to tricarboxylic acid cycle, Succinate, pyruvate/inositol catabolism, α aminobutyrate metabolism, regulators, exported and cell surface molecules, multi drug exporters, and heat and cold shock proteins (early induced) fix genes, nif (late induced). | Karunakaran et al., 2009 | |
| Erwinia chrysanthemi (soft rot) | Chrysanthemum leaves extract | 2-DE, MALDI-TOF MS | 25 | Endopectate lyases, pectin acetyl esterases, pectin methylesterase, poly galacturonase, flagellin, and elongation factor. | Kazemi-Pour et al., 2004 |
| Agrobacterium tumefaciens | 200 μM acetosyringone (As) | 2-DE, MALDI-Q-TOF MS | 11 | As induced vir proteins, type IV secretion system (T4SS), newly As-induced proteins regulated by the virA/virG, an unknown protein Y4mC, and heat shock protein. | Lai et al., 2006 |
| Streptomyces coelicolor | Lemna minor fronds | 2-DE, MALDI-TOF MS | 31 | Differential proteins of S. coelicolor with and without L. minor fronds in minimal medium: proteins related to energy, metabolism, protein synthesis, proteins involved in the acquisition of carbon, stress-induced (chaperonin, ATP-GTP binding protein, tellurite resistance protein, and Fe superoxide dismutase). | Langlois et al., 2003 |
| S. meliloti strain 2011 | Medicago truncatula/3–6 D for drought | LC MS/MS | 377 | Proteins accumulated in M. truncatula in vivo with S. meliloti under drought: protein synthesis/degradation, stress proteins, RNA regulation, secondary metabolism, signaling, amino acid carbohydrate, nucleic acid/hormone metabolism, glycolysis/tricarboxylic acid cycle. | Larrainzar et al., 2007 |
| Streptomyces scabies | potato suberin, lipidic plant polymer | 2-DE, Protein sequencer MS/MS | 19 | Differential proteins in S. scabies in minimal media with and without 0.2% potato suberin: proteins with increased abundance in response to suberin (Nucleotide and amino acid metabolism, glycolysis/tricarboxylic acid cycle enzymes, chaperonin, phenylacetaldehyde dehydrogenase, fructose-bisphosphate aldolase, triose phosphate isomerase, ABC transporter, ATPase subunit, lipoprotein, and serine hydroxymethyl transferase). | Lauzier et al., 2008 |
| Frankia sp. strain CcI3 (Symbiont) | Casuarina cunninghamiana and C. glauca/Alnus incana and Elaeagnus angustifolia | 2-DE, MS/MS, LC MS/MS | 73/53 | Frankia strains in root nodules of Alnus incana and Elaeagnus angustifolia (cell wall/growth enzymes, solute-binding proteins (amino acids, peptides, inorganic ions) (ABC transporter, molybdate binding proteins, Leu/Ile/Val/Glu/Thr-binding protein precursor, hydrolytic enzymes, proteins involved in cell processes (DNA polymerase, signal transduction histidine, and T2SS protein). | Mastronunzio et al., 2009 |
| Pectobacterium atrosepticum (Pathogen in potato) | Potato stem/tubers extract | 2-DE, MALDI-TOF MS | 40 | Abundant proteins in minimal medium with potato tuber extracts: (T3SS protein, pectin enzymes, vir protein Svx, flagellar hook associated protein, endo-polygalacturonase, dihydrolipoamide dehydrogenase, hexosaminidase, pectate lyase, fructose bisphosphate aldolase, ABC transporter, glyceraldehyde 3-phosphate dehydrogenase, and chaperones). | Mattinen et al., 2007 |
| Ralstonia solanacearum UW551 (phylotype II) and GMI1000 | S. lycopersicum cv. Bonny Best | Microarray | 109 by HrpB | Enhancement of hrpB regulated genes via T3SS, sucrose uptake and catabolism via SCR ABC, sucrose dependent phosphoenol pyruvate-carbohydrate phosphotransferase, glycolysis enzymes, cell wall-degrading enzymes, exopolysaccharide, reactive oxygen species, inorganic, organic and aminoacid and nucleic acid metabolic enzymes, tricarboxylic acid cycle intermediates, and pentose phosphate pathway. | Jacobs et al., 2012 |
| B. japonicum USDA110 (Symbiont) | G. max L. Merrill cultivar Akishirome. 7–49 DAI | 2-DE, MALDI-TOF MS | 275 | Proteins accumulation related to transcription, Nif and Fix proteins, translation, protein folding, and degradation, synthetic enzyme of the poly-beta-hydroxybutyrate, solute transporter, and elongation factor-thermo unstable. | Nomura et al., 2010 |
| A. tumefaciens. C58 strain ATCC 33970 | Solanum lycopersicum cv. Rutgers stem, roots | 2-DE, MALDI-TOF MS | 30 | Augmentation of ABC transporter, ATPase protein, alcohol dehydrogenase, enoyl CoA hydratase/isomerase, aldehyde dehydrogenase, protein-L-isoaspartate O-methyltransferase, acetyl COA carboxylase, ribosomal proteins (chaperonin, hydrolases, and sugar-binding protein), and aldolase. | Rosen et al., 2003 |
| B. japonicum USDA110 | HM medium (Cole and Elkan, 1973)/root nodule residing B. japonicum | 2-DE, MALDI-TOF MS | 1200 | Suppression of fatty acid, nucleic acid and cell surface synthesis, DNA metabolism-related proteins and proteolytic enzymes. Enhancement of translation, transcription related proteins, elongation factor, chaperones (heat shock protein, chaperonin), ATP synthase, DNA polymerase, and nitrogen metabolism proteins. | Sarma and Emerich, 2006 |
| B. japonicum USDA110 | G. max. cv. Williams 82. Nodule protein | 2-DE, MALDI-TOF MS | 180 | Augmentation of proteins related to nitrogen, carbon metabolism, protein synthesis, scaffolding and degradation, cellular detoxification function (ATP synthetase, elongation factor ribosomal protein, chaperonin, heat shock protein), stress regulation, signaling communication. Decline of fatty acid and nucleic acid metabolism, solute transport (ABC transporter) proteins, protein synthesis, scaffolding and degradation, cellular detoxification, stress regulation and signaling communication. | Sarma and Emerich, 2005 |
| B. japonicum | G. max, Vigna unguiculata and Macroptilium atropurpureum | LC-MS/MS | 2000 | Accumulation of housekeeping proteins, ribosomal proteins, ABC-type transporter sulfonate-binding protein, enoyl-CoA hydratase, transketolase, hydroxyphenylpyruvate dioxygenase, nitropropane dioxygenase. | Koch et al., 2010 |
| Xylella fastidiosa strain 9a5c | Brazilian sweet orange | 2-DE, MALDI-TOF MS | 30 | Synthesis of aconitate hydratase, DNAk protein, dihydrolipoamide dehydrogenase, lipase/esterase, 30S, 50S ribosomal protein, inosine-5′-monophosphate dehydrogenase, heat shock protein, peptidyl-prolyl cis-trans isomerase, ATP synthase, aspartate-B-semialdehyde dehydrogenase, alcohol dehydrogenase, fructose-bisphosphate aldolase, malate dehydrogenase, ABC transporter ATP-binding protein, chaperone, elongation factor, and RNA polymerase. | Smolka et al., 2003 |
| Xanthomonas citri subsp. citri | TSE medium (with sucrose and glutamic acid) induce pathogenesity | 2-DE, LC MS/MS | 1702 | Expression of Hrp gene dependent T3SS enzymes, tricarboxylic acid cycle, glycolysis/gluconeogenesis, pentose phosphate pathway, other sugar metabolism, urea cycle, pyrimidine and purine biosynthesis, fatty acid synthesis and degradation pathways, polyamine biosynthesis, DNA, RNA, protein metabolism, initiation, elongation, transcription, translation factors, cell structure and function, division, transport, pathogenesis and vir. | Soares et al., 2010 |
| X. campestris pv. campestris B100 | 2-DE, MALDI-TOF MS | 87 | Accumulation of outer membrane proteins with signal peptide, ATP synthase beta chain, 30s ribosomal protein, metabolic proteins, protein maintenance and folding (chaperonin, DNA k), and degradive enzymes (cellulase, lipase). | Watt et al., 2005 | |
| Pantoea stewartii subsp. stewartii (Pnss) vir/P. stewartii subsp. indologenes (Pnsi) avir | Stewart's bacterial wilt and leaf blight of maize and sweet corn | 2-DE, LC MS/MS, MALDI-TOF MS | 21 | Proteins accumulation in virulent verses avirulent strain: siderophore-based iron uptake system, motility, adhesion, and biofilm formation (flagellin B homolog), pilus adhesion, transdolase, secretory protein (T3SS protein, HrcJ, 60 kDa chaperonin), mannosyl transferase, transdolase, LysR, transcriptional activator belonging to the AraC family, ABC transporter. | Wu et al., 2007 |
| A. tumefaciens | LC MS/MS | 12 | Enhancement of T4SS secretome proteins, virB, hemolysin- coregulated protein, periplasmic binding protein, amino acid-binding periplasmic protein, hemin-binding lipoprotein, and dipeptide protein. | Wu et al., 2008 | |
| S. meliloti mutants 2011-3.4 and 1021Δhfq | Alfalfa | 2-DE, MALDI-TOF MS | 33 | Proteins lower in abundance were sugar transporters, enzymes of central carbon metabolism, glycine betaine, electron transport chain, iron, sugar catabolism, biosynthesis of aminoacids, vitamins, purines and pyrimidines, chaperonin, heat shock protein, and ABC transporter. Proteins augmented were metabolism of nitrogen sources (mainly amino acids), glycine cleavage system, metabolic enzymes such as ornithine cyclodeaminase, arginase, adenosylhomocysteinase, and phosphoenol pyruvate carboxykinase. | Torres-Quesada et al., 2010 |
1
IP: Number of identified protein.
Abbreviations: DAI, days after inoculation; ATP, adenine triphosphate; As, Acetosyringone; vir, virulence; T3SS, Type III secretion system; T4SS, Type IV secretion system; 2-DE, two-dimensional polyacrylamide gel electrophoresis; MS, Mass spectrometry; MS/MS, Tandom Mass spectrometry; MALDI-TOF, Matrix-assisted laser desorption/ionization time of flight; LC, liquid chromatography.