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Volumn 6, Issue FEB, 2015, Pages

Advantages and limitations of shot-gun proteomic analyses on Arabidopsis plants with altered MAPK signaling

Author keywords

Mitogen activated protein kinase (MAPK); Phosphoproteomics; Proteomics; Shot gun proteomics; Signaling; Validation

Indexed keywords

ARABIDOPSIS;

EID: 84925060076     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2015.00107     Document Type: Article
Times cited : (9)

References (31)
  • 1
    • 84873377702 scopus 로고    scopus 로고
    • A Versatile mass spectrometry-based method to both identify kinase client-relationships and characterize signaling network topology
    • Ahsan, N., Huang, Y., Tovar-Mendez, A., Swatek, K. N., Zhang, J., Miernyk, J. A., et al. (2013). A Versatile mass spectrometry-based method to both identify kinase client-relationships and characterize signaling network topology. J. Proteome Res. 12, 937-948. doi: 10.1021/pr3009995
    • (2013) J. Proteome Res , vol.12 , pp. 937-948
    • Ahsan, N.1    Huang, Y.2    Tovar-Mendez, A.3    Swatek, K.N.4    Zhang, J.5    Miernyk, J.A.6
  • 2
    • 49849090995 scopus 로고    scopus 로고
    • A simple and rapid technique for detecting protein phosphorylation using one-dimensional isoelectric focusing gels and immunoblot analysis
    • Anderson, J. C., and Peck, S. C. (2008). A simple and rapid technique for detecting protein phosphorylation using one-dimensional isoelectric focusing gels and immunoblot analysis. Plant J. 55, 881-885. doi: 10.1111/j.1365-313X.2008.03550.x
    • (2008) Plant J , vol.55 , pp. 881-885
    • Anderson, J.C.1    Peck, S.C.2
  • 3
    • 84857518627 scopus 로고    scopus 로고
    • Biological sequence motif discovery using motif-x
    • Chapter 13, Unit 13
    • Chou, M. F., and Schwartz, D. (2011). Biological sequence motif discovery using motif-x. Curr. Protoc. Bioinformatics Chapter 13, Unit 13. 15-24. doi: 10.1002/0471250953.bi1315s35
    • (2011) Curr. Protoc. Bioinformatics , pp. 15-24
    • Chou, M.F.1    Schwartz, D.2
  • 4
    • 43949138227 scopus 로고    scopus 로고
    • Blast2GO: A comprehensive suite for functional analysis in plant genomics
    • Conesa, A., and Götz, S. (2008). Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics 2008:619832. doi: 10.1155/2008/619832
    • (2008) Int. J. Plant Genomics , vol.2008
    • Conesa, A.1    Götz, S.2
  • 5
    • 84877099986 scopus 로고    scopus 로고
    • Knockout of AtMKK1 enhances salt tolerance and modifies metabolic activities in Arabidopsis
    • Conroy, C., Ching, J., Gao, Y., Wang, X., Rampitsch, C., and Xing, T. (2013). Knockout of AtMKK1 enhances salt tolerance and modifies metabolic activities in Arabidopsis. Plant Signal. Behav. 8:e24206. doi: 10.4161/psb.24206
    • (2013) Plant Signal. Behav , vol.8
    • Conroy, C.1    Ching, J.2    Gao, Y.3    Wang, X.4    Rampitsch, C.5    Xing, T.6
  • 6
    • 3142756502 scopus 로고    scopus 로고
    • Open source clustering software
    • de Hoon, M. J. L., Imoto, S., Nolan, J., and Miyano, S. (2004). Open source clustering software. Bioinformatics 20, 1453-1454. doi: 10.1093/bioinformatics/bth078
    • (2004) Bioinformatics , vol.20 , pp. 1453-1454
    • de Hoon, M.J.L.1    Imoto, S.2    Nolan, J.3    Miyano, S.4
  • 7
    • 55849107369 scopus 로고    scopus 로고
    • Towards functional phosphoproteomics by mapping differential phosphorylation events in signaling networks
    • de la Fuente van Bentem, S., Mentzen, W. I., de la Fuente, A., and Hirt, H. (2008). Towards functional phosphoproteomics by mapping differential phosphorylation events in signaling networks. Proteomics 8, 4453-4465. doi: 10.1002/pmic.200800175
    • (2008) Proteomics , vol.8 , pp. 4453-4465
    • van de la Fuente Bentem, S.1    Mentzen, W.I.2    de la Fuente, A.3    Hirt, H.4
  • 8
    • 27644573819 scopus 로고    scopus 로고
    • High throughput identification of potential Arabidopsis mitogen-activated protein kinases substrates
    • Feilner, T., Hultschig, C., Lee, J., Meyer, S., Immink, R. G. H., Koenig, A., et al. (2005). High throughput identification of potential Arabidopsis mitogen-activated protein kinases substrates. Mol. Cell. Proteomics 4, 1558-1568. doi: 10.1074/mcp.M500007-MCP200
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1558-1568
    • Feilner, T.1    Hultschig, C.2    Lee, J.3    Meyer, S.4    Immink, R.G.H.5    Koenig, A.6
  • 9
    • 84912127570 scopus 로고    scopus 로고
    • Functional analysis of Arabidopsis immune-related MAPKs uncovers a role for MPK3 as negative regulator of inducible defences
    • Freidit Frey, N., Garcia, A. V., Bigeard, J., Zaag, R., Bueso, E., Garmier, M., et al. (2014). Functional analysis of Arabidopsis immune-related MAPKs uncovers a role for MPK3 as negative regulator of inducible defences. Genome Biol. 15:R87. doi: 10.1186/gb-2014-15-6-r87
    • (2014) Genome Biol , vol.15
    • Freidit Frey, N.1    Garcia, A.V.2    Bigeard, J.3    Zaag, R.4    Bueso, E.5    Garmier, M.6
  • 10
    • 0033016717 scopus 로고    scopus 로고
    • Correlation between protein and mRNA abundance in yeast
    • Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. (1999). Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720-1730.
    • (1999) Mol. Cell. Biol , vol.19 , pp. 1720-1730
    • Gygi, S.P.1    Rochon, Y.2    Franza, B.R.3    Aebersold, R.4
  • 11
    • 84874092435 scopus 로고    scopus 로고
    • Identification of novel in vivo MAP kinase substrates in Arabidopsis thaliana through use of tandem metal oxide affinity chromatography
    • Hoehenwarter, W., Thomas, M., Nukarinen, E., Egelhofer, V., Röhrig, H., Weckwerth, W., et al. (2013). Identification of novel in vivo MAP kinase substrates in Arabidopsis thaliana through use of tandem metal oxide affinity chromatography. Mol. Cell. Proteomics 12, 369-380. doi: 10.1074/mcp.M112.020560
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 369-380
    • Hoehenwarter, W.1    Thomas, M.2    Nukarinen, E.3    Egelhofer, V.4    Röhrig, H.5    Weckwerth, W.6
  • 14
    • 58149193234 scopus 로고    scopus 로고
    • STRING 8-a global view on proteins and their functional interactions in 630 organisms
    • Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., et al. (2009). STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 37, D412-D416. doi: 10.1093/nar/gkn760
    • (2009) Nucleic Acids Res , vol.37 , pp. D412-D416
    • Jensen, L.J.1    Kuhn, M.2    Stark, M.3    Chaffron, S.4    Creevey, C.5    Muller, J.6
  • 15
    • 84867057236 scopus 로고    scopus 로고
    • Analysing signalling networks by mass spectrometry
    • Jørgensen, C., and Locard-Paulet, M. (2012). Analysing signalling networks by mass spectrometry. Amino Acids43, 1061-1074. doi: 10.1007/s00726-012-1293-z
    • (2012) Amino Acids , vol.43 , pp. 1061-1074
    • Jørgensen, C.1    Locard-Paulet, M.2
  • 16
    • 33645714857 scopus 로고    scopus 로고
    • Phosphate-binding tag, a new tool to visualize phosphorylated proteins
    • Kinoshita, E., Kinoshita-Kikuta, E., Takiyama, K., and Koike, T. (2006). Phosphate-binding tag, a new tool to visualize phosphorylated proteins. Mol. Cell. Proteomics 5, 749-757. doi: 10.1074/mcp.T500024-MCP200
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 749-757
    • Kinoshita, E.1    Kinoshita-Kikuta, E.2    Takiyama, K.3    Koike, T.4
  • 17
    • 84922482161 scopus 로고    scopus 로고
    • Affinity-Based SDS PAGE identification of phosphorylated Arabidopsis MAPKs and substrates by acrylamide pendant Phos-TAG™
    • Komis, G., Takáč, T., Bekešová, S., Vadovič, P., and Samaj, J. (2014). Affinity-Based SDS PAGE identification of phosphorylated Arabidopsis MAPKs and substrates by acrylamide pendant Phos-TAG™. Methods Mol. Biol. 1171, 47-63. doi: 10.1007/978-1-4939-0922-3_5
    • (2014) Methods Mol. Biol , vol.1171 , pp. 47-63
    • Komis, G.1    Takáč, T.2    Bekešová, S.3    Vadovič, P.4    Samaj, J.5
  • 18
    • 0036016411 scopus 로고    scopus 로고
    • An Arabidopsis mitogen-activated protein kinase kinase kinase gene family encodes essential positive regulators of cytokinesis
    • Krysan, P. J., Jester, P. J., Gottwald, J. R., and Sussman, M. R. (2002). An Arabidopsis mitogen-activated protein kinase kinase kinase gene family encodes essential positive regulators of cytokinesis. Plant Cell 14, 1109-1120. doi: 10.1105/tpc.001164
    • (2002) Plant Cell , vol.14 , pp. 1109-1120
    • Krysan, P.J.1    Jester, P.J.2    Gottwald, J.R.3    Sussman, M.R.4
  • 19
    • 84908227339 scopus 로고    scopus 로고
    • Sustained mitogen-activated protein kinase activation reprograms defense metabolism and phosphoprotein profile in Arabidopsis thaliana
    • Lassowskat, I., Böttcher, C., Eschen-Lippold, L., Scheel, D., and Lee, J. (2014). Sustained mitogen-activated protein kinase activation reprograms defense metabolism and phosphoprotein profile in Arabidopsis thaliana. Front. Plant Sci. 5:554. doi: 10.3389/fpls.2014.00554
    • (2014) Front. Plant Sci , vol.5 , pp. 554
    • Lassowskat, I.1    Böttcher, C.2    Eschen-Lippold, L.3    Scheel, D.4    Lee, J.5
  • 20
    • 67650102675 scopus 로고    scopus 로고
    • Quantitative proteomics identifies oxidant-induced, AtMPK6-dependent changes in Arabidopsis thaliana protein profiles
    • Miles, G. P., Samuel, M. A., Ranish, J. A., Donohoe, S. M., Sperrazzo, G. M., and Ellis, B. E. (2009). Quantitative proteomics identifies oxidant-induced, AtMPK6-dependent changes in Arabidopsis thaliana protein profiles. Plant Signal. Behav. 4, 497-505. doi: 10.4161/psb.4.6.8538
    • (2009) Plant Signal. Behav , vol.4 , pp. 497-505
    • Miles, G.P.1    Samuel, M.A.2    Ranish, J.A.3    Donohoe, S.M.4    Sperrazzo, G.M.5    Ellis, B.E.6
  • 21
    • 77951879057 scopus 로고    scopus 로고
    • Coexpression landscape in ATTED-II: Usage of gene list and gene network for various types of pathways
    • Obayashi, T., and Kinoshita, K. (2010). Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways. J. Plant Res. 123, 311-319. doi: 10.1007/s10265-010-0333-6
    • (2010) J. Plant Res , vol.123 , pp. 311-319
    • Obayashi, T.1    Kinoshita, K.2
  • 22
    • 84901389957 scopus 로고    scopus 로고
    • Salt-induced subcellular kinase relocation and seedling susceptibility caused by overexpression of Medicago SIMKK in Arabidopsis
    • Ovečka, M., Takáč, T., Komis, G., Vadovič, P., Bekešová, S., Doskočilová, A., et al. (2014). Salt-induced subcellular kinase relocation and seedling susceptibility caused by overexpression of Medicago SIMKK in Arabidopsis. J. Exp. Bot. 65, 2335-2350. doi: 10.1093/jxb/eru115
    • (2014) J. Exp. Bot , vol.65 , pp. 2335-2350
    • Ovečka, M.1    Takáč, T.2    Komis, G.3    Vadovič, P.4    Bekešová, S.5    Doskočilová, A.6
  • 23
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: Discriminating signal peptides from transmembrane regions
    • Petersen, T. N., Brunak, S., von Heijne, G., and Nielsen, H. (2011). SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785-786. doi: 10.1038/nmeth.1701
    • (2011) Nat. Methods , vol.8 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    von Heijne, G.3    Nielsen, H.4
  • 24
    • 58149498875 scopus 로고    scopus 로고
    • MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays
    • Popescu, S. C., Popescu, G. V., Bachan, S., Zhang, Z., Gerstein, M., Snyder, M., et al. (2009). MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev. 23, 80-92. doi: 10.1101/gad.1740009
    • (2009) Genes Dev , vol.23 , pp. 80-92
    • Popescu, S.C.1    Popescu, G.V.2    Bachan, S.3    Zhang, Z.4    Gerstein, M.5    Snyder, M.6
  • 25
    • 84865842504 scopus 로고    scopus 로고
    • Rice mitogen-activated protein kinase interactome analysis using the yeast two-hybrid system
    • Singh, R., Lee, M.-O., Lee, J.-E., Choi, J., Park, J. H., Kim, E. H., et al. (2012). Rice mitogen-activated protein kinase interactome analysis using the yeast two-hybrid system. Plant Physiol. 160, 477-487. doi: 10.1104/pp.112.200071
    • (2012) Plant Physiol , vol.160 , pp. 477-487
    • Singh, R.1    Lee, M.-O.2    Lee, J.-E.3    Choi, J.4    Park, J.H.5    Kim, E.H.6
  • 26
    • 84905121389 scopus 로고    scopus 로고
    • Involvement of YODA and mitogen activated protein kinase 6 in Arabidopsis post-embryogenic root development through auxin up-regulation and cell division plane orientation
    • Smékalová, V., Luptovčiak, I., Komis, G., Šamajová, O., Ovečka, M., Doskočilová, A., et al. (2014). Involvement of YODA and mitogen activated protein kinase 6 in Arabidopsis post-embryogenic root development through auxin up-regulation and cell division plane orientation. New Phytol. 203, 1175-1193. doi: 10.1111/nph.12880
    • (2014) New Phytol , vol.203 , pp. 1175-1193
    • Smékalová, V.1    Luptovčiak, I.2    Komis, G.3    Šamajová, O.4    Ovečka, M.5    Doskočilová, A.6
  • 27
    • 34447133519 scopus 로고    scopus 로고
    • Tomato mitogen-activated protein kinases LeMPK1, LeMPK2, and LeMPK3 are activated during the cf-4/avr4-induced hypersensitive response and have distinct phosphorylation specificities
    • Stulemeijer, I. J. E., Stratmann, J. W., and Joosten, M. H. A. J. (2007). Tomato mitogen-activated protein kinases LeMPK1, LeMPK2, and LeMPK3 are activated during the cf-4/avr4-induced hypersensitive response and have distinct phosphorylation specificities. Plant Physiol. 144, 1481-1494. doi: 10.1104/pp.107.101063
    • (2007) Plant Physiol , vol.144 , pp. 1481-1494
    • Stulemeijer, I.J.E.1    Stratmann, J.W.2    Joosten, M.H.A.J.3
  • 28
    • 84885233035 scopus 로고    scopus 로고
    • Vesicular trafficking and stress response coupled to PI3K inhibition by LY294002 as revealed by proteomic and cell biological analysis
    • Takáč, T., Pechan, T., Šamajová, O., and Šamaj, J. (2013). Vesicular trafficking and stress response coupled to PI3K inhibition by LY294002 as revealed by proteomic and cell biological analysis. J. Proteome Res. 12, 4435-4448. doi: 10.1021/pr400466x
    • (2013) J. Proteome Res , vol.12 , pp. 4435-4448
    • Takáč, T.1    Pechan, T.2    Šamajová, O.3    Šamaj, J.4
  • 29
    • 84861833367 scopus 로고    scopus 로고
    • Wortmannin treatment induces changes in Arabidopsis root proteome and post-golgi compartments
    • Takáč, T., Pechan, T., Samajova, O., Ovecka, M., Richter, H., Eck, C., et al. (2012). Wortmannin treatment induces changes in Arabidopsis root proteome and post-golgi compartments. J. Proteome Res. 11, 3127-3142. doi: 10.1021/pr201111n
    • (2012) J. Proteome Res , vol.11 , pp. 3127-3142
    • Takáč, T.1    Pechan, T.2    Samajova, O.3    Ovecka, M.4    Richter, H.5    Eck, C.6
  • 30
    • 84915751026 scopus 로고    scopus 로고
    • Proteomic and biochemical analyses show functional network of proteins involved in antioxidant defense of Arabidopsis anp2anp3 double mutant
    • Takáč, T., Šamajová, O., Vadovič, P., Pechan, T., Košútová, P., Ovečka, M., et al. (2014). Proteomic and biochemical analyses show functional network of proteins involved in antioxidant defense of Arabidopsis anp2anp3 double mutant. J. Proteome Res. 13, 5347-5361. doi: 10.1021/pr500588c
    • (2014) J. Proteome Res , vol.13 , pp. 5347-5361
    • Takáč, T.1    Šamajová, O.2    Vadovič, P.3    Pechan, T.4    Košútová, P.5    Ovečka, M.6
  • 31
    • 84890677480 scopus 로고    scopus 로고
    • Stable isotope metabolic labeling-based quantitative phosphoproteomic analysis of Arabidopsis mutants reveals ethylene-regulated time-dependent phosphoproteins putative substrates of constitutive triple response 1 kinase
    • Yang, Z., Guo, G., Zhang, M., Liu, C. Y., Hu, Q., Lam, H., et al. (2013). Stable isotope metabolic labeling-based quantitative phosphoproteomic analysis of Arabidopsis mutants reveals ethylene-regulated time-dependent phosphoproteins putative substrates of constitutive triple response 1 kinase. Mol. Cell. Proteomics 12, 3559-3582. doi: 10.1074/mcp.M113.031633
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 3559-3582
    • Yang, Z.1    Guo, G.2    Zhang, M.3    Liu, C.Y.4    Hu, Q.5    Lam, H.6


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