A Cautionary note on the use of split-YFP/BiFC in plant protein-protein interaction studies

International Journal of Molecular Sciences

Volumn 15, Issue 6, 2014, Pages 9628-9643

  Horstman, Anneke ^a   Tonaco, Isabella Antonia Nougalli ^a   Boutilier, Kim ^a   Immink, Richard G H ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Bimolecular fluorescence complementation (BiFC); Fluorescence microscopy; In planta; Protein complementation assay (PCA); Protein protein interaction; Split YFP (yellow fluorescent protein)

Indexed keywords

YELLOW FLUORESCENT PROTEIN; BACTERIAL PROTEIN; FLUORESCENT DYE; PHOTOPROTEIN; VEGETABLE PROTEIN; YELLOW FLUORESCENT PROTEIN, BACTERIA;

AMINO ACID SEQUENCE; BIMOLECULAR FLUORESCENCE COMPLEMENTATION METHOD; CELL TYPE; CHEMICAL PROCEDURES; CONFOCAL LASER MICROSCOPY; CONTROLLED STUDY; FLUORESCENCE MICROSCOPY; GENE VECTOR; GENETIC COMPLEMENTATION; NONHUMAN; NOTE; POINT MUTATION; PROTEIN ASSEMBLY; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; WESTERN BLOTTING; GENETIC TRANSFECTION; GENETICS; METABOLISM; PLANT; PROCEDURES; PROTEIN ANALYSIS;

BACTERIAL PROTEINS; FLUORESCENT DYES; GENETIC VECTORS; LUMINESCENT PROTEINS; MICROSCOPY, FLUORESCENCE; PLANT PROTEINS; PLANTS; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; TRANSFECTION;

EID: 84901844570     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms15069628     Document Type: Note

References (42)

1. Braun, P.; Aubourg, S.; van Leene, J.; de Jaeger, G.; Lurin, C. Plant Protein Interactomes. Annu. Rev. Plant Biol. 2013, 64, 161-187.
2. Immink, R.G.H.; Angenent, G.C. Transcription factors do it together: the hows and whys of studying protein-protein interactions. Trends Plant Sci. 2002, 7, 531-534.
3. Kodama, Y.; Hu, C.-D. Bimolecular fluorescence complementation (BiFC): A 5-year update and future perspectives. BioTechniques 2012, 53, 285-298.
4. Ghosh, I.; Hamilton, A.D.; Regan, L. Antiparallel leucine zipper-directed protein reassembly: Application to the green fluorescent protein. J. Am. Chem. Soc. 2000, 122, 5658-5659.
5. Hu, C.-D.; Chinenov, Y.; Kerppola, T.K. Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol. Cell 2002, 9, 789-798.
6. Bracha-Drori, K.; Shichrur, K.; Katz, A.; Oliva, M.; Angelovici, R.; Yalovsky, S.; Ohad, N. Detection of protein-protein interactions in plants using bimolecular fluorescence complementation. Plant J. 2004, 40, 419-427.
7. Walter, M.; Chaban, C.; Schütze, K.; Batistic, O.; Weckermann, K.; Näke, C.; Blazevic, D.; Grefen, C.; Schumacher, K.; Oecking, C.; et al. Visualization of protein interactions in living plant cells using bimolecular fluorescence complementation. Plant J. 2004, 40, 428-438.
8. Kerppola, T.K. Multicolor Bimolecular Fluorescence Complementation (BiFC) Analysis of Protein Interactions with Alternative Partners. Cold Spring Harb. Protoc. 2013, 2013, doi:10.1101/pdb.top077164.
9. Lee, L.-Y.; Fang, M.-J.; Kuang, L.-Y.; Gelvin, S. Vectors for multi-color bimolecular fluorescence complementation to investigate protein-protein interactions in living plant cells. Plant Methods 2008, 4, doi:10.1186/1746-4811-4-24.
10. Waadt, R.; Schmidt, L.K.; Lohse, M.; Hashimoto, K.; Bock, R.; Kudla, J. Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta. Plant J. 2008, 56, 505-516.
11. Shyu, Y.J.; Suarez, C.D.; Hu, C.-D. Visualization of ternary complexes in living cells by using a BiFC-based FRET assay. Nat. Protoc. 2008, 3, 1693-1702.
12. Shyu, Y.J.; Suarez, C.D.; Hu, C.-D. Visualization of AP-1-NF-κB ternary complexes in living cells by using a BiFC-based FRET. Proc. Natl. Acad. Sci. USA 2008, 105, 151-156.
13. Smaczniak, C.; Immink, R.G.H.; Muiño, J.M.; Blanvillain, R.; Busscher, M.; Busscher-Lange, J.; Dinh, Q.D.; Liu, S.; Westphal, A.H.; Boeren, S.; et al. Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development. Proc. Natl. Acad Sci. USA 2012, 109, 1560-1565.
14. Ohashi, K.; Kiuchi, T.; Shoji, K.; Sampei, K.; Mizuno, K. Visualization of cofilin-actin and Ras-Raf interactions by bimolecular fluorescence complementation assays using a new pair of split Venus fragments. BioTechniques 2012, 52, 45-50.
15. Kodama, Y.; Hu, C.-D., An improved bimolecular fluorescence complementation assay with a high signal-to-noise ratio. BioTechniques 2010, 49, 793-805.
16. Nakagawa, C.; Inahata, K.; Nishimura, S.; Sugimoto, K. Improvement of a venus-based bimolecular fluorescence complementation assay to visualize bFos-bJun interaction in living cells. Biosci. Biotechnol. Biochem. 2011, 75, 1399-1401.
17. Kerppola, T.K. Design and implementation of bimolecular fluorescence complementation (BiFC) assays for the visualization of protein interactions in living cells. Nat. Protoc. 2006, 1, 1278-1286.
18. Fang, Y.; Spector, D.L. BiFC imaging assay for plant protein-protein interactions. Cold Spring Harb. Protoc. 2010, 2010, doi:10.1101/pdb.prot5380.
19. Saka, Y.; Hagemann, A.I.; Smith, J.C. Visualizing protein interactions by bimolecular fluorescence complementation in Xenopus. Methods 2008, 45, 192-195.
20. PubMed-NCBI: US National Library of Medicine National Institutes of Health. Available online: http://www.ncbi.nlm.nih.gov/pubmed (accessed on 1 February 2014).
21. Lee, L.Y.; Wu, F.H.; Hsu, C.T.; Shen, S.C.; Yeh, H.Y.; Liao, D.C.; Fang, M.J.; Liu, N.T.; Yen, Y.C.; Dokladal, L.; et al. Screening a cDNA library for protein-protein interactions directly in planta. Plant Cell 2012, 24, 1746-1759.
22. Arai, R.; Ueda, H.; Kitayama, A.; Kamiya, N.; Nagamune, T. Design of the linkers which effectively separate domains of a bifunctional fusion protein. Protein Eng. 2001, 14, 529-532.
23. Welch, D.; Hassan, H.; Blilou, I.; Immink, R.; Heidstra, R.; Scheres, B. Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action. Genes Dev. 2007, 21, 2196-2204.
24. Hartley, J.L.; Temple, G.F.; Brasch, M.A. DNA cloning using in vitro site-specific recombination. Genome Res. 2000, 10, 1788-1795.
25. Busso, D.; Dleagoutte-Busso, B.; Moras, D. Construction of a set gateway-based destination vectors for high-throughput cloning and expression screening in Eschericia coli. Anal. Biochem. 2005, 343, 313-321.
26. Jang, C.; Seo, E.Y.; Nam, J.; Bae, H.; Gim, Y.G.; Kim, H.G.; Cho, I.S.; Lee, Z.W.; Bauchan, G.R.; Hammond, J.; et al. Insights into alternanthera mosaic virus TGB3 functions: Interactions with nicotiana benthamiana PsbO correlate with chloroplast vesiculation and veinal necrosis caused by TGB3 over-expression. Front. Plant Sci. 2013, 4, doi:10.3389/fpls.2013.00005.
27. Park, M.-R.; Kim, K.-H. Molecular characterization of the interaction between the N-terminal region of Potato virus X (PVX) coat protein (CP) and Nicotiana benthamiana PVX CP-interacting protein, NbPCIP1. Virus Genes 2013, 46, 517-523.
28. Dong, C.H.; Jang, M.; Scharein, B.; Malach, A.; Rivarola, M.; Liesch, J.; Groth, G.; Hwang, I.; Chang, C. Molecular association of the Arabidopsis ETR1 ethylene receptor and a regulator of ethylene signaling, RTE1. J. Biol. Chem. 2010, 285, 40706-40713.
29. Ren, X.L.; Qi, G.N.; Feng, H.Q.; Zhao, S.; Zhao, S.S.; Wang, Y.; Wu, W.H. Calcineurin B-like protein CBL10 directly interacts with AKT1 and modulates K+ homeostasis in Arabidopsis. Plant J. Cell Mol. Biol. 2013, 74, 258-266.
30. Merzlyak, E.M.; Goedhart, J.; Shcherbo, D.; Bulina, M.E.; Shcheglov, A.S.; Fradkov, A.F.; Gaintzeva, A.; Lukyanov, K.A.; Lukyanov, S.; Gadella, T.W.J.; et al. Bright monomeric red fluorescent protein with an extended fluorescence lifetime. Nat. Methods 2007, 4, 555-557.
31. Boutilier, K.; Offringa, R.; Sharma, V.K.; Kieft, H.; Ouellet, T.; Zhang, L.; Hattori, J.; Liu, C.-M.; van Lammeren, A.A.M.; Miki, B.L.A.; et al. Ectopic Expression of BABY BOOM Triggers a Conversion from Vegetative to Embryonic Growth. Plant Cell 2002, 14, 1737-1749.
32. Boevink, P.; McLellan, H.; Bukharova, T.; Engelhardt, S.; Birch, P. In vivo protein-protein interaction studies with BiFC: Conditions, cautions, and caveats. Methods Mol. Biol. 2014, 1127, 81-90.
33. Schutze, K.; Harter, K.; Chaban, C. Bimolecular fluorescence complementation (BiFC) to study protein-protein interactions in living plant cells. Methods Mol. Biol. 2009, 479, 189-202.
34. Waadt, R.; Kudla, J. In planta visualization of protein interactions using bimolecular fluorescence complementation (BiFC). CSH Protoc. 2008, 2008, doi:10.1101/pdb.prot4995.
35. Denecke, J.; Gossele, V.; Botterman, J.; Cornelissen, M. Quantitative analysis of transiently expressed genes in plant cells. Methods Mol. Cell. Biol. 1989, 1, 19-27.
36. Immink, R.G.H.; Gadella, T.W.J.; Ferrario, S.; Busscher, M.; Angenent, G.C. Analysis of MADS box protein-protein interactions in living plant cells. Proc. Natl. Acad. Sci. USA 2002, 99, 2416-2421.
37. Tonaco, I.A.N.; Borst, J.W.; de Vries, S.C.; Angenent, G.C.; Immink, R.G.H. In vivo imaging of MADS-box transcription factor interactions. J. Exp. Bot. 2006, 57, 33-42.
38. Shyu, Y.J.; Liu, H.; Deng, X.; Hu, C.-D. Identification of new fluorescent protein fragments for bimolecular fluorescence complementation analysis under physiological conditions. BioTechniques 2006, 40, 61-66.
39. Berendzen, K.W.; Bohmer, M.; Wallmeroth, N.; Peter, S.; Vesic, M.; Zhou, Y.; Tiesler, F.K.E.; Schleifenbaum, F.; Harter, K. Screening for in planta protein-protein interactions combining bimolecular fluorescence complementation with flow cytometry. Plant Methods 2012, 8, doi:10.1186/1746-4811-8-25.
40. Denecke, J.; Vitale, A. The use of protoplasts to study protein synthesis and transport by the plant endomembrane system. Methods Cell Biol. 1995, 50, 335-348.
41. Bücherl, C.; Aker, J.; Vries, S.; Borst, J.W. Probing protein-protein interactions with FRET-FLIM. Methods Mol. Biol. 2010, 655, 389-399.
42. Morsy, M.; Gouthu, S.; Orchard, S.; Thorneycroft, D.; Harper, J.F.; Mittler, R.; Cushman, J.C. Charting plant interactomes: possibilities and challenges. Trends Plant Sci. 2008, 13, 183-191.