Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues

Abstract

Proteins are the cell’s functional entities. Rather than operating independently, they interact with other proteins. Capturing in vivo protein complexes is therefore crucial to gain understanding of the function of a protein in a cellular context. Affinity purification coupled to mass spectrometry has proven to yield a wealth of information about protein complex constitutions for a broad range of organisms. For Oryza sativa, the technique has been initiated in callus and shoots, but has not been optimized ever since. We translated an optimized tandem affinity purification (TAP) approach from Arabidopsis thaliana toward Oryza sativa, and demonstrate its applicability in a variety of rice tissues. A list of non-specific and false positive interactors is presented, based on re-occurrence over more than 170 independent experiments, to filter bona fide interactors. We demonstrate the sensitivity of our approach by isolating the complexes for the rice ANAPHASE PROMOTING COMPLEX SUBUNIT 10 (APC10) and CYCLIN-DEPENDENT KINASE D (CDKD) proteins from the proliferation zone of the emerging fourth leaf. Next to APC10 and CDKD, we tested several additional baits in the different rice tissues and reproducibly retrieved at least one interactor for 81.4 % of the baits screened for in callus tissue and T1 seedlings. By transferring an optimized TAP tag combined with state-of-the-art mass spectrometry, our TAP protocol enables the discovery of interactors for low abundance proteins in rice and opens the possibility to capture complex dynamics by comparing tissues at different stages of a developing rice organ.

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Abbreviations

AP–MS:

Affinity purification coupled to mass spectrometry

TAP:

Tandem affinity purification

APC10:

ANAPHASE PROMOTING COMPLEX SUBUNIT 10

CDKD:

CYCLIN-DEPENDENT KINASE D

PPI:

Protein–protein interaction

Y2H:

Yeast two-hybrid

ORF:

Open reading frame

PCA:

Protein complementation analysis

RING:

REALLY INTERESTING NEW GENE

CCS52A:

CELL CYCLE SWITCH PROTEIN 52 A

CAK:

CDK-activating kinase

CYCH:

CYCLIN H

MAT1:

MENAGE A TROIS

TFIIH:

General transcription factor II H

XPB:

XERODERMA PIGMENTOSUM B

XPD:

XERODERMA PIGMENTOSUM D

SBP:

Streptavidin-binding peptide

MS:

Mass spectrometry

TEV:

Tobacco etch virus

IgG:

Immunoglobulin G

RAP:

Rice annotation project

MSU:

Michigan State University

CBP:

Calmodulin-binding peptide

EGTA:

Ethylene glycol tetra-acetic acid

References

  1. Abe M, Fujiwara M, Kurotani K-I, Yokoi S, Shimamoto K (2008) Identification of dynamin as an interactor of rice GIGANTEA by tandem affinity purification (TAP). Plant Cell Physiol 49:420–432. doi:10.1093/pcp/pcn019

    CAS  Article  PubMed  Google Scholar 

  2. Boruc J, Van den Daele H, Hollunder J, Rombauts S, Mylle E, Hilson P, Inzé D, De Veylder L, Russinova E (2010) Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network. Plant Cell 22:1264–1280. doi:10.1105/tpc.109.073635

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  3. Boudolf V, Rombauts S, Naudts M, Inzé D, De Veylder L (2001) Identification of novel cyclin-dependent kinases interacting with the CKS1 protein of Arabidopsis. J Exp Bot 52:1381–1382

    CAS  Article  PubMed  Google Scholar 

  4. Braun P, Carvunis AR, Charloteaux B, Dreze M, Ecker JR, Hill DE, Roth FP, Vidal M, Galli M, Balumuri P, Bautista V, Chesnut JD, Kim RC, de los Reyes C, Gilles P, Kim CJ, Matrubutham U, Mirchandani J, Olivares E, Patnaik S, Quan R, Ramaswamy G, Shinn P, Sw VM (2011) Evidence for network evolution in an Arabidopsis interactome map. Science 333:601–607. doi:10.1126/science.1203877

    CAS  Article  Google Scholar 

  5. Bürckstümmer T, Bennett KL, Preradovic A, Schütze G, Hantschel O, Superti-Furga G, Bauch A (2006) An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells. Nat Methods 3:1013–1019. doi:10.1038/nmeth968

    Article  PubMed  Google Scholar 

  6. Capron A, Serralbo O, Fülöp K, Frugier F, Parmentier Y, Dong A, Lecureuil A, Guerche P, Kondorosi E, Scheres B, Genschik P (2003) The Arabidopsis anaphase-promoting complex or cyclosome: molecular and genetic characterization of the APC2 subunit. Plant Cell 15:2370–2382. doi:10.1105/tpc.013847

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25:288–289. doi:10.1093/bioinformatics/btn615

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. Chang WH, Kornberg RD (2000) Electron crystal structure of the transcription factor and DNA repair complex, core TFIIH. Cell 102:609–613

    CAS  Article  PubMed  Google Scholar 

  9. Chang L, Zhang Z, Yang J, McLaughlin SH, Barford D (2014) Molecular architecture and mechanism of the anaphase-promoting complex. Nature 513:388–393. doi:10.1038/nature13543

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. Christensen AH, Sharrock RA, Quail PH (1992) Maize polyubiquitin genes: structure, thermal perturbation of expression and transcript splicing, and promoter activity following transfer to protoplasts by electroporation. Plant Mol Biol 18:675–689

    CAS  Article  PubMed  Google Scholar 

  11. De Veylder L, Beeckman T, Beemster GT, Krols L, Terras F, Landrieu I, van der Schueren E, Maes S, Naudts M, Inzé D (2001) Functional analysis of cyclin-dependent kinase inhibitors of Arabidopsis. Plant Cell 13:1653–1668

    Article  PubMed  PubMed Central  Google Scholar 

  12. Dedecker M, Van Leene J, De Jaeger G (2015) Unravelling plant molecular machineries through affinity purification coupled to mass spectrometry. Curr Opin Plant Biol 24:1–9. doi:10.1016/j.pbi.2015.01.001

    CAS  Article  PubMed  Google Scholar 

  13. Ding X, Richter T, Chen M, Fujii H, Seo YS, Xie M, Zheng X, Kanrar S, Stevenson RA, Dardick C, Li Y, Jiang H, Zhang Y, Yu F, Bartley LE, Chern M, Bart R, Chen X, Zhu L, Farmerie WG, Gribskov M, Zhu J-K, Fromm ME, Ronald PC, Song W-Y (2009) A rice kinase-protein interaction map. Plant Physiol 149:1478–1492. doi:10.1104/pp.108.128298

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. Dong H, Fei G-L, Wu C-Y, Wu F-Q, Sun Y-Y, Chen M-J, Ren Y-L, Zhou K-N, Cheng Z-J, Wang J-L, Jiang L, Zhang X, Guo X-P, Lei C-L, Su N, Wang H, Wan J-M (2013) A rice virescent-yellow leaf mutant reveals new insights into the role and assembly of plastid caseinolytic protease in higher plants. Plant Physiol 162:1867–1880. doi:10.1104/pp.113.217604

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. Eloy NB, Coppens F, Beemster GTS, Hemerly AS, Ferreira PCG (2006) The Arabidopsis anaphase promoting complex (APC): regulation through subunit availability in plant tissues. Cell Cycle 5:1957–1965

    CAS  Article  PubMed  Google Scholar 

  16. Eloy NB, Gonzalez N, Van Leene J, Maleux K, Vanhaeren H, De Milde L, Dhondt S, Vercruysse L, Witters E, Mercier R, Cromer L, Beemster GTS, Remaut H, Van Montagu MCE, De Jaeger G, Ferreira PCG, Inzé D (2012) 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. doi:10.1073/pnas.1211418109

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. Fabian-Marwedel T, Umeda M, Sauter M (2002) The rice cyclin-dependent kinase-activating kinase R2 regulates S-phase progression. Plant Cell 14:197–210. doi:10.1105/tpc.010386

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  18. Gadeyne A, Sánchez-Rodríguez C, Vanneste S, Di Rubbo S, Zauber H, Vanneste K, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Mayers JR, Adamowski M, Kania U, Ehrlich M, Schweighofer A, Ketelaar T, Maere S, Bednarek SY, Friml J, Gevaert K, Witters E, Russinova E, Persson S, De Jaeger G, Van Damme D (2014) The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell 156:691–704. doi:10.1016/j.cell.2014.01.039

    CAS  Article  PubMed  Google Scholar 

  19. Gibbons BJ, Brignole EJ, Azubel M, Murakami K, Voss NR, Bushnell DA, Asturias FJ, Kornberg RD (2012) Subunit architecture of general transcription factor TFIIH. Proc Natl Acad Sci USA 109:1949–1954. doi:10.1073/pnas.1105266109

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. Gibson TJ, Seiler M, Veitia RA (2013) The transience of transient overexpression. Nat Methods 10:715–721. doi:10.1038/nmeth.2534

    CAS  Article  PubMed  Google Scholar 

  21. Heyman J, De Veylder L (2012) The anaphase-promoting complex/cyclosome in control of plant development. Mol Plant 5:1182–1194. doi:10.1093/mp/sss094

    CAS  Article  PubMed  Google Scholar 

  22. Jacqmard A, De Veylder L, Segers G, de Almeida EJ, Bernier G, Van Montagu M, Inze D (1999) Expression of CKS1At in Arabidopsis thaliana indicates a role for the protein in both the mitotic and the endoreduplication cycle. Planta 207:496–504

    CAS  Article  PubMed  Google Scholar 

  23. Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (NY) 6:4. doi:10.1186/1939-8433-6-4

    Article  Google Scholar 

  24. Keilhauer EC, Hein MY, Mann M (2015) Accurate protein complex retrieval by affinity enrichment mass spectrometry (AE-MS) rather than affinity purification mass spectrometry (AP–MS). Mol Cell Proteomics 14:120–135. doi:10.1074/mcp.M114.041012

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. Lima MDF, Eloy NB, Pegoraro C, Sagit R, Rojas C, Bretz T, Vargas L, Elofsson A, de Oliveira AC, Hemerly AS, Ferreira PC (2010) Genomic evolution and complexity of the anaphase-promoting complex (APC) in land plants. BMC Plant Biol 10:254. doi:10.1186/1471-2229-10-254

    Article  PubMed Central  Google Scholar 

  26. Lin Q, Wang D, Dong H, Gu S, Cheng Z, Gong J, Qin R, Jiang L, Li G, Wang JL, Wu F, Guo X, Zhang X, Lei C, Wang H, Wan J (2012) Rice APC/C(TE) controls tillering by mediating the degradation of MONOCULM 1. Nat Commun 3:752. doi:10.1038/ncomms1716

    Article  PubMed  PubMed Central  Google Scholar 

  27. Lumba S, Toh S, Handfield L-F, Swan M, Liu R, Youn J-Y, Cutler SR, Subramaniam R, Provart N, Moses A, Desveaux D, McCourt P (2014) A mesoscale abscisic acid hormone interactome reveals a dynamic signaling landscape in Arabidopsis. Dev Cell 29:360–372. doi:10.1016/j.devcel.2014.04.004

    CAS  Article  PubMed  Google Scholar 

  28. Nallamilli BRR, Zhang J, Mujahid H, Malone BM, Bridges SM, Peng Z (2013) Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development and grain filling via a mechanism distinct from Arabidopsis. PLoS Genet 9:e1003322. doi:10.1371/journal.pgen.1003322

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  29. Rohila JS, Chen M, Chen S, Chen J, Cerny R, Dardick C, Canlas P, Xu X, Gribskov M, Kanrar S, Zhu J-K, Ronald P, Fromm ME (2006) Protein–protein interactions of tandem affinity purification-tagged protein kinases in rice. Plant J 46:1–13. doi:10.1111/j.1365-313X.2006.02671.x

    CAS  Article  PubMed  Google Scholar 

  30. Rohila JS, Chen M, Chen S, Chen J, Cerny RL, Dardick C, Canlas P, Fujii H, Gribskov M, Kanrar S, Knoflicek L, Stevenson B, Xie M, Xu X, Zheng X, Zhu J-K, Ronald P, Fromm ME (2009) Protein–protein interactions of tandem affinity purified protein kinases from rice. PLoS ONE 4:e6685. doi:10.1371/journal.pone.0006685

    Article  PubMed  PubMed Central  Google Scholar 

  31. Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang C, Iwamoto M, Abe T, Yamada Y, Muto A, Inokuchi H, Ikemura T, Matsumoto T, Sasaki T, Itoh T (2013) Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol 54:e6. doi:10.1093/pcp/pcs183

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. Schultz P, Fribourg S, Poterszman A, Mallouh V, Moras D, Egly JM (2000) Molecular structure of human TFIIH. Cell 102:599–607

    CAS  Article  PubMed  Google Scholar 

  33. Seo Y-S, Chern M, Bartley LE, Han M, Jung K-H, Lee I, Walia H, Richter T, Xu X, Cao P, Bai W, Ramanan R, Amonpant F, Arul L, Canlas PE, Ruan R, Park C-J, Chen X, Hwang S, Jeon J-S, Ronald PC (2011) Towards establishment of a rice stress response interactome. PLoS Genet 7:e1002020. doi:10.1371/journal.pgen.1002020

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. Shimotohno A, Umeda-Hara C, Bisova K, Uchimiya H, Umeda M (2004) The plant-specific kinase CDKF;1 is involved in activating phosphorylation of cyclin-dependent kinase-activating kinases in Arabidopsis. Plant Cell 16:2954–2966. doi:10.1105/tpc.104.025601

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  35. Smaczniak C, Immink RGH, Muiño JM, Blanvillain R, Busscher M, Busscher-Lange J, Dinh QDP, Liu S, Westphal AH, Boeren S, Parcy F, Xu L, Carles CC, Angenent GC, Kaufmann K (2012) Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development. Proc Natl Acad Sci USA 109:1560–1565. doi:10.1073/pnas.1112871109

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K (2012) Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol 158:590–600. doi:10.1104/pp.111.189514

    Article  PubMed  PubMed Central  Google Scholar 

  37. Van Leene J, Stals H, Eeckhout D, Persiau G, Van De Slijke E, Van Isterdael G, De Clercq A, Bonnet E, Laukens K, Remmerie N, Henderickx K, De Vijlder T, Abdelkrim A, Pharazyn A, Van Onckelen H, Inzé D, Witters E, De Jaeger G (2007) A tandem affinity purification-based technology platform to study the cell cycle interactome in Arabidopsis thaliana. Mol Cell Proteomics 6:1226–1238. doi:10.1074/mcp.M700078-MCP200

    Article  PubMed  Google Scholar 

  38. Van Leene J, Witters E, Inzé D, De Jaeger G (2008) Boosting tandem affinity purification of plant protein complexes. Trends Plant Sci 13:517–520. doi:10.1016/j.tplants.2008.08.002

    Article  PubMed  Google Scholar 

  39. Van Leene J, Hollunder J, Eeckhout D, Persiau G, Van De Slijke E, Stals H, Van Isterdael G, Verkest A, Neirynck S, Buffel Y, De Bodt S, Maere S, Laukens K, Pharazyn A, Ferreira PCG, Eloy N, Renne C, Meyer C, Faure J-D, Steinbrenner J, Beynon J, Larkin JC, Van de Peer Y, Hilson P, Kuiper M, De Veylder L, Van Onckelen H, Inzé D, Witters E, De Jaeger G (2010) Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol Syst Biol 6:397. doi:10.1038/msb.2010.53

    PubMed  PubMed Central  Google Scholar 

  40. Van Leene J, Eeckhout D, Cannoot B, De Winne N, Persiau G, Van De Slijke E, Vercruysse L, Dedecker M, Verkest A, Vandepoele K, Martens L, Witters E, Gevaert K, De Jaeger G (2015) An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes. Nat Protoc 10:169–187. doi:10.1038/nprot.2014.199

    Article  PubMed  Google Scholar 

  41. Vanstraelen M, Baloban M, Da O, Cultrone A, Lammens T, Brown SC, De VL, Mergaert P, Kondorosi E (2009) APC/C CCS52A complexes control meristem maintenance in the Arabidopsis root. Proc Natl Acad Sci USA 106(28):11806–11811. doi:10.1073/pnas.0901193106

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  42. Vercruyssen L, Verkest A, Gonzalez N, Heyndrickx KS, Eeckhout D, Han S-K, Jégu T, Archacki R, Van Leene J, Andriankaja M, De Bodt S, Abeel T, Coppens F, Dhondt S, De Milde L, Vermeersch M, Maleux K, Gevaert K, Jerzmanowski A, Benhamed M, Wagner D, Vandepoele K, De Jaeger G, Inzé D (2014) ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. Plant Cell 26:210–229. doi:10.1105/tpc.113.115907

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  43. Xu C, Wang Y, Yu Y, Duan J, Liao Z, Xiong G, Meng X, Liu G, Qian Q, Li J (2012) Degradation of MONOCULM 1 by APC/C(TAD1) regulates rice tillering. Nat Commun 3:750. doi:10.1038/ncomms1743

    Article  PubMed  PubMed Central  Google Scholar 

  44. Yamaguchi M, Umeda M, Uchimiya H (1998) A rice homolog of Cdk7/MO15 phosphorylates both cyclin-dependent protein kinases and the carboxy-terminal domain of RNA polymerase II. Plant J 16:613–619

    CAS  Article  PubMed  Google Scholar 

  45. Zhong J, Haynes PA, Zhang S, Yang X, Andon NL, Eckert D, Yates JR, Wang X, Budworth P (2003) Development of a system for the study of protein–protein interactions in planta: characterization of a TATA-box binding protein complex in Oryza sativa. J Proteome Res 2:514–522

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Acknowledgments

Maarten Dedecker is supported by a predoctoral fellowship from the Agency for Innovation by Science and Technology and CropDesign N.V. (‘Baekeland’ funding, IWT 100222). The authors thank Annick Bleys for help in preparing the manuscript.

Author contributions

M.D., S.V. and G.D.J. designed the research. N.D.W., G.P., E.V.D.S, B.C., L.V., L.D. and N.W. performed experiments. M.D., D.E. and G.D.J. analyzed the data. K.G. provided protocols for LC–MS/MS analysis. J.V.L. and K.G. commented on the manuscript. M.D. and G.D.J. wrote the manuscript.

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Correspondence to Maarten Dedecker or Geert De Jaeger.

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Dedecker, M., Van Leene, J., De Winne, N. et al. Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues. Plant Mol Biol 91, 341–354 (2016). https://doi.org/10.1007/s11103-016-0471-x

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Keywords

  • Anaphase promoting complex
  • CYCLIN-DEPENDENT KINASE D
  • Oryza sativa (rice)
  • Protein–protein interactions
  • Tandem affinity purification coupled to mass spectrometry (TAP–MS)