An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes (original) (raw)

• Braun, P., Aubourg, S., Van Leene, J., De Jaeger, G. & Lurin, C. Plant protein interactomes. Annu. Rev. Plant Biol. 64, 161–187 (2013).
  Article CAS PubMed Google Scholar
• Van Leene, J., Boruc, J., De Jaeger, G., Russinova, E. & De Veylder, L. A kaleidoscopic view of the _Arabidopsis_core cell cycle interactome. Trends Plant Sci. 16, 141–150 (2011).
  Article CAS PubMed Google Scholar
• Arabidopsis Interactome Mapping Consortium. Evidence for network evolution in an Arabidopsis interactome map. Science 333, 601–607 (2011).
• Backstrom, S., Elfving, N., Nilsson, R., Wingsle, G. & Bjorklund, S. Purification of a plant mediator from Arabidopsis thaliana identifies PFT1 as the Med25 subunit. Mol. Cell 26, 717–729 (2007).
  Article PubMed CAS Google Scholar
• Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183 (2002).
  Article CAS PubMed Google Scholar
• Witte, C.P., Noel, L.D., Gielbert, J., Parker, J.E. & Romeis, T. Rapid one-step protein purification from plant material using the eight-amino acid StrepII epitope. Plant Mol. Biol. 55, 135–147 (2004).
  Article CAS PubMed Google Scholar
• Smaczniak, C. et al. Proteomics-based identification of low-abundance signaling and regulatory protein complexes in native plant tissues. Nat. Protoc. 7, 2144–2158 (2012).
  Article CAS PubMed Google Scholar
• Fröhlich, A. et al. Looking deep inside: detection of low-abundance proteins in leaf extracts of Arabidopsis and phloem exudates of pumpkin. Plant Physiol. 159, 902–914 (2012).
  Article PubMed PubMed Central CAS Google Scholar
• Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030–1032 (1999).
  Article CAS PubMed Google Scholar
• Van Leene, J., Witters, E., Inzé, D. & De Jaeger, G. Boosting tandem affinity purification of plant protein complexes. Trends Plant Sci. 13, 517–520 (2008).
  Article CAS PubMed Google Scholar
• Puig, O. et al. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218–229 (2001).
  Article CAS PubMed Google Scholar
• Kühner, S. et al. Proteome organization in a genome-reduced bacterium. Science 326, 1235–1240 (2009).
  Article PubMed CAS Google Scholar
• Gavin, A.-C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636 (2006).
  Article CAS PubMed Google Scholar
• Krogan, N.J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637–643 (2006).
  Article CAS PubMed Google Scholar
• Hutchins, J.R.A. et al. Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science 328, 593–599 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Butland, G. et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531–537 (2005).
  Article CAS PubMed Google Scholar
• Van Leene, J. et al. Isolation of transcription factor complexes from Arabidopsis cell suspension cultures by tandem affinity purification. Methods Mol. Biol. 754, 195–218 (2011).
  Article CAS PubMed Google Scholar
• Van Leene, J. et al. A tandem affinity purification-based technology platform to study the cell cycle interactome in Arabidopsis thaliana. Mol. Cell. Proteomics 6, 1226–1238 (2007).
  Article CAS PubMed Google Scholar
• Takahashi, N. et al. The DNA replication checkpoint aids survival of plants deficient in the novel replisome factor ETG1. EMBO J. 27, 1840–1851 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Takahashi, N. et al. The MCM-binding protein ETG1 aids sister chromatid cohesion required for postreplicative homologous recombination repair. PLoS Genet. 6, e1000817 (2010).
  Article PubMed PubMed Central CAS Google Scholar
• Pauwels, L. et al. NINJA connects the co-repressor TOPLESS to jasmonate signalling. Nature 464, 788–791 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Gadeyne, A. et al. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell 156, 691–704 (2014).
  Article CAS PubMed Google Scholar
• Spinner, L. et al. A protein phosphatase 2A complex spatially controls plant cell division. Nat. Commun. 4, 1863 (2013).
  Article PubMed CAS Google Scholar
• Van Leene, J. et al. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol. Syst. Biol. 6, 397 (2010).
  Article PubMed PubMed Central CAS Google Scholar
• Eloy, N.B. et al. SAMBA, a plant-specific anaphase-promoting complex/cyclosome regulator is involved in early development and A-type cyclin stabilization. Proc. Natl. Acad. Sci. USA 109, 13853–13858 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Heyman, J. et al. Arabidopsis ULTRAVIOLET-B-INSENSITIVE4 maintains cell division activity by temporal inhibition of the anaphase-promoting complex/cyclosome. Plant Cell 23, 4394–4410 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Heyman, J. et al. ERF115 controls root quiescent center cell division and stem cell replenishment. Science 342, 860–863 (2013).
  Article CAS PubMed Google Scholar
• Bürckstümmer, T. et al. An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells. Nat. Methods 3, 1013–1019 (2006).
  Article PubMed CAS Google Scholar
• Vercruyssen, L. et al. ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. Plant Cell 26, 210–229 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Lamesch, P. et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 40, D1202–D1210 (2012).
  Article CAS PubMed Google Scholar
• Xu, X. et al. The tandem affinity purification method: an efficient system for protein complex purification and protein interaction identification. Protein Expr. Purif. 72, 149–156 (2010).
  Article CAS PubMed Google Scholar
• Li, Y. The tandem affinity purification technology: an overview. Biotechnol. Lett. 33, 1487–1499 (2011).
  Article CAS PubMed Google Scholar
• Kyriakakis, P., Tipping, M., Abed, L. & Veraksa, A. Tandem affinity purification in _Drosophila_—the advantages of the GS-TAP system. Fly 2, 229–235 (2008).
  Article PubMed Google Scholar
• Ma, H. et al. A highly efficient multifunctional tandem affinity purification approach applicable to diverse organisms. Mol. Cell. Proteomics 11, 501–511 (2012).
  Article PubMed PubMed Central CAS Google Scholar
• Li, F. et al. Structure of the core editing complex (L-complex) involved in uridine insertion/deletion RNA editing in trypanosomatid mitochondria. Proc. Natl. Acad. Sci. USA 106, 12306–12310 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Sundberg, M. et al. The heteromultimeric debranching enzyme involved in starch synthesis in Arabidopsis requires both isoamylase1 and isoamylase2 subunits for complex stability and activity. PLoS ONE 8, e75223 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Heijde, M. et al. Constitutively active UVR8 photoreceptor variant in Arabidopsis. Proc. Natl. Acad. Sci. USA 110, 20326–20331 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Benhamed, M. et al. Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. Plant J. 56, 493–504 (2008).
  Article CAS PubMed Google Scholar
• Domenichini, S. et al. Evidence for a role of Arabidopsis CDT1 proteins in gametophyte development and maintenance of genome integrity. Plant Cell 24, 2779–2791 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Van Damme, D. et al. Adaptin-like protein TPLATE and clathrin recruitment during plant somatic cytokinesis occurs via two distinct pathways. Proc. Natl. Acad. Sci. USA 108, 615–620 (2011).
  Article CAS PubMed Google Scholar
• Boudolf, V. et al. CDKB1;1 forms a functional complex with CYCA2;3 to suppress endocycle onset. Plant Physiol. 150, 1482–1493 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Van Aken, O. et al. Mitochondrial type-I prohibitins of Arabidopsis thaliana are required for supporting proficient meristem development. Plant J. 52, 850–864 (2007).
  Article CAS PubMed Google Scholar
• Cromer, L. et al. Centromeric cohesion is protected twice at meiosis, by SHUGOSHINs at anaphase I and by PATRONUS at interkinesis. Curr. Biol. 23, 2090–2099 (2013).
  Article CAS PubMed Google Scholar
• Berckmans, B. et al. Auxin-dependent cell cycle reactivation through transcriptional regulation of Arabidopsis E2Fa by lateral organ boundary proteins. Plant Cell 23, 3671–3683 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Nelissen, H. et al. Plant Elongator regulates auxin-related genes during RNA polymerase II transcription elongation. Proc. Natl. Acad. Sci. USA 107, 1678–1683 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Fernández-Calvo, P. et al. The Arabidopsis bHLH transcription factors MYC3 and MYC4 are targets of JAZ repressors and act additively with MYC2 in the activation of jasmonate responses. Plant Cell 23, 701–715 (2011).
  Article PubMed PubMed Central CAS Google Scholar
• Geerinck, J., Pauwels, L., De Jaeger, G. & Goossens, A. Dissection of the one-megaDalton JAZ1 protein complex. Plant Signal. Behav. 5, 1039–1041 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Antoni, R. et al. PYRABACTIN RESISTANCE1-LIKE8 plays an important role for the regulation of abscisic acid signaling in root. Plant Physiol. 161, 931–941 (2013).
  Article CAS PubMed Google Scholar
• Di Rubbo, S. et al. The clathrin adaptor complex AP-2 mediates endocytosis of BRASSINOSTEROID INSENSITIVE1 in Arabidopsis. Plant Cell 25, 2986–2997 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Sauer, M. et al. MTV1 and MTV4 encode plant-specific ENTH and ARF GAP proteins that mediate clathrin-dependent trafficking of vacuolar cargo from the _trans_-Golgi network. Plant Cell 25, 2217–2235 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Nodzyński, T. et al. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Mol. Plant 6, 1849–1862 (2013).
  Article PubMed CAS Google Scholar
• Bassard, J.-E. et al. Protein-protein and protein-membrane associations in the lignin pathway. Plant Cell 24, 4465–4482 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Menges, M. & Murray, J.A.H. Synchronous _Arabidopsis_suspension cultures for analysis of cell-cycle gene activity. Plant J. 30, 203–212 (2002).
  Article CAS PubMed Google Scholar
• Verkest, A. et al. A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification. Plant Physiol. 164, 1122–1133 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Gibson, T.J., Seiler, M. & Veitia, R.A. The transience of transient overexpression. Nat. Methods 10, 715–721 (2013).
  Article CAS PubMed Google Scholar
• Facette, M.R., Shen, Z., Björnsdóttir, F.R., Briggs, S.P. & Smith, L.G. Parallel proteomic and phosphoproteomic analyses of successive stages of maize leaf development. Plant Cell 25, 2798–2812 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, G., Wu, W.W., Zhang, Z., Masilamani, S. & Shen, R.-F. Decoy methods for assessing false positives and false discovery rates in shotgun proteomics. Anal. Chem. 81, 146–159 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Van Bel, M. et al. Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol. 158, 590–600 (2012).
  Article CAS PubMed Google Scholar
• Carbon, S. et al. AmiGO: online access to ontology and annotation data. Bioinformatics 25, 288–289 (2009).
  Article CAS PubMed Google Scholar
• Pardo, M. & Choudhary, J.S. Assignment of protein interactions from affinity purification/mass spectrometry data. J. Proteome Res. 11, 1462–1474 (2012).
  Article CAS PubMed Google Scholar
• Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, X., Henriques, R., Lin, S.-S., Niu, Q.-W. & Chua, N.-H. _Agrobacterium_-mediated transformation of _Arabidopsis thaliana_using the floral dip method. Nat. Protoc. 1, 641–646 (2006).
  Article CAS PubMed Google Scholar
• Clough, S.J. & Bent, A.F. Floral dip: a simplified method for _Agrobacterium_-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).
  Article CAS PubMed Google Scholar
• Hubner, N.C. et al. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J. Cell Biol. 189, 739–754 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Horiguchi, G., Kim, G.-T. & Tsukaya, H. The transcription factor AtGRF5 and the transcription coactivator AN3 regulate cell proliferation in leaf primordia of Arabidopsis thaliana. Plant J. 43, 68–78 (2005).
  Article CAS PubMed Google Scholar
• De Bodt, S., Hollunder, J., Nelissen, H., Meulemeester, N. & Inzé, D. CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations. New Phytol. 195, 707–720 (2012).
  Article CAS PubMed Google Scholar