Kaede for detection of protein oligomerization

Molecular Plant

Volumn 6, Issue 5, 2013, Pages 1453-1462

  Wolf, Heike ^a   Barisas, B George ^b   Dietz, Karl Josef ^a   Seidel, Thorsten ^a  

^a BIELEFELD UNIVERSITY   (Germany)

^b Veterinary Dentistry and Oral Surgery   (United States)

Author keywords

fluorescence imaging; protein structure; protein protein interaction

Indexed keywords

VERTEBRATA;

HYBRID PROTEIN; KAEDE PROTEIN, TRACHYPHYLLIA GEOFFROYI; PEROXIREDOXIN; PHOTOPROTEIN;

ARTICLE; CELL FRACTIONATION; FLUORESCENCE IMAGING; FLUORESCENCE RESONANCE ENERGY TRANSFER; LASER; LIGHT; LIGHT RELATED PHENOMENA; METABOLISM; PLANT CELL; PLASMID; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN TRANSPORT; PROTEIN-PROTEIN INTERACTION; RADIATION EXPOSURE;

FLUORESCENCE IMAGING; PROTEIN STRUCTURE; PROTEIN-PROTEIN INTERACTION;

FLUORESCENCE RESONANCE ENERGY TRANSFER; LASERS; LIGHT; LUMINESCENT PROTEINS; OPTICAL PHENOMENA; PEROXIREDOXINS; PLANT CELLS; PLASMIDS; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN STABILITY; PROTEIN TRANSPORT; RECOMBINANT FUSION PROTEINS; SUBCELLULAR FRACTIONS;

EID: 84885041942     PISSN: 16742052     EISSN: 17529867     Source Type: Journal    
DOI: 10.1093/mp/sst039     Document Type: Article

References (52)

1. Akrap, N., Seidel, T., and Barisas, B.G. (2010). Förster distances for fluorescence resonant energy transfer between mCherry and other visible fluorescent proteins. Anal. Biochem. 402, 105-106.
2. Ando, R., Hama, H., Yamamoto-Hino, M., Mizuno, H., and Miyawaki, A. (2002). An optical marker based on the UV-induced green to red photoconversion of a fluorescent protein. Proc. Natl Acad. Sci. U S A. 99, 12651-12656.
3. Arimura, S., Yamamoto, J., Aida, G.P., Nakazono, M., and Tsutsumi, N. (2004). Frequent fusion and fission of plant mitochondria with unequal nucleoid distribution. Proc. Natl Acad. Sci. U S A. 101, 7805-7808.
4. Barondeau, D.P., Kassmann, C.J., Tainer, J.A., and Getzoff, E.D. (2006). Understanding GFP posttranslational chemistry: structures of designed variants that achieve backbone fragmentation, hydrolysis, and decarboxylation. J. Am. Chem. Soc. 128, 4685-4693.
5. Billinton, N., and Knight, A.W. (2001). Seeing the wood through the trees: a review of techniques for distinguishing green fluorescent protein from endogenous autofluorescence. Analyt. Biochem. 291, 175-197.
6. Brown, J.L., Snir, M., Noushmehr, H., Kirby, M., Hong, S.K., Elkahloun, A.G., and Feldman, B. (2008). Transcriptional profiling of endogenous germ layer precursor cells identifies dusp4 as an essential gene in zebrafish endosperm specification. Proc. Natl. Acad. Sci. U S A. 105, 12337-12342.
7. Brown, S.C., Bolte, S., Gaudin, M., Pereira, C., Marion, J., Soler, M.N., and Satiat-Jeunemaitre, B. (2010). Exploring plant endomembrane dynamics using the photoconvertible protein Kaede. Plant J. 63, 696-711.
8. Christie, J.M. (2007). Phototropin blue-light receptors. Annu. Rev. Plant Biol. 58, 21-45.
9. Dietz, K.J. (2011). Peroxiredoxins in plants and cyanobacteria. Antioxid. Redox Signal. 15, 1129-1159.
10. Dittrich, P.S., Schäfer, S.P., and Schwille, P. (2005). Characterization of the photoconversion on reaction of the fluorescent protein Kaede on the single-molecule level. Biophys. J. 89, 3446-3455.
11. Earley, K.W., Haag, J.R., Pontes, O., Opper, K., Juehne, T., Song, K., and Pikaard, C.S. (2006). Gateway-compatible vectors for plant functional genomics and proteomics. Plant J. 45, 616-629.
12. Gadella, T.W. Jr., van der Krogt, G.N., and Bisseling, T. (1999). GFP-based FRET microscopy in living plant cells. Trends Plant Sci. 4, 287-291.
13. Gurskaya, N.G., Verkhusha, V.V., Shcheglov, A.S., Staroverov, D.B., Chepurnykh, T.V., Fradkov, A.F., Lukyanov, S., and Lukyanov, K.A. (2006). Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light. Nat. Biotechnol. 24, 461-465.
14. Harter, K., Meixner, A.J., and Schleifenbaum, F. (2012). Spectromicroscopy of living plant cell. Mol. Plant. 5, 14-26.
15. Hatta, K., Tsujii, H., and Omura, T. (2006). Cell tracking using a photoconvertible fluorescent protein. Nat. Protoc. 1, 960-967.
16. Hayashi, I., Mizuno, H., Tong, K.I., Furuta, T., Tanaka, F., Yoshimura, M., Miyawaki, A., and Ikura, M. (2007). Crystallographic evidence for water-assisted photo-induced peptide cleavage in the stony coral fluorescent protein Kaede. J. Mol. Biol. 372, 918-926.
17. Hosoi, H., Mizuno, H., Miyawaki, A., and Tahara, T. (2006). Competition between energy and proton transfer in ultrafast excited-state dynamics of an oligomeric fluorescent protein red Kaede. J. Phys. Chem. B. 110, 22853-22860.
18. Kami, C., Lorrain, S., Horniteschek, P., and Fankhauser, C. (2010). Light-regulated plant growth and development. Curr. Top. Developm. Biol. 91, 29-66.
19. Kasahara, M., Swartz, T.E., Olney, M.A., Onodera, A., Mochizuki, N., Fukuzawa, H., Asamizu, E., Tabata, S., Kanegae, H., Takano, M., et al. (2002). Photochemical properties of the flavin mononucleotide binding domains of the phototropins from Arabidopsis, rice and Chlamydomonas reinhardtii. Plant Physiol. 129, 762-773.
20. Kremers, G.J., and Goedhart, J. (2009). Visible fluorescent proteins for FRET. Laboratory Techn. Biochem. Mol. Biol. 33, 171-224.
21. Kremers, G.J., Hazelwood, K.L., Murphy, C.S., Davidson, M.W., and Piston, D.W. (2009). Photoconversion in orange and red fluorescent proteins. Nat. Methods. 6, 355-358.
22. Leung, K.M., and Holt, C.E. (2008). Live visualization of protein synthesis in axonal growth cones by microinjection of photoconvertible Kaede in Xenopus embryos. Nat. Protoc. 3, 1318-1327.
23. Liu, H., Liu, B., Zhao, C., Pepper, M., and Lin, C. (2011). The action mechanisms of plant cryptochromes. Trends Plant Sci. 16, 684-691.
24. Mizohata, E., Sakai, H., Fusatomi, E., Terada, T., Murayama, K., Shirouzu, M., and Yokoyama, S. (2005). Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aerypyrum pernix K1. J. Mol. Biol. 354, 317-332.
25. Mizuno, H., Mal, T.K., Tong, K.I., Ando, R., Furuta, T., Ikura, M., and Miyawaki, A. (2003). Photo-induced peptide cleavage in the green-to-red conversion of a fluorescent protein. Mol. Cell. 12, 1051-1058.
26. Moon, J.C., Hah, Y.S., Kim, W.Y., Jung, B.G., Lee, J.R., Kim, S.Y., Lee, Y.M., Jeon, M.G., Kim, C.W., Cho, M.J., and Lee, S.Y. (2005). Oxidative stress-dependent structural and functional switching of a human 2-Cys peroxiredoxin isotype II that enhances HeLa cell resistance to H2O2-induced cell death. J. Biol. Chem. 280, 28775-28784.
27. Muthuramalingam, M., Seidel, T., Laxa, M., Nunes de Miranda, S.M., Gärtner, F., Ströher, E., Kandlbinder, A., and Dietz, K.J. (2009). Multiple redox and non-redox interactions define 2-Cys peroxiredoxin as a regulatory hub in the chloroplast. Mol. Plant. 2, 1273-1288.
28. Mutoh, T., Miyata, T., Kashiwagi, S., Miyawaki, A., and Ogawa, M. (2006). Dynamic behaviour of individual cells in developing organotypic brain slices revealed by the photoconvertable protein Kaede. Exp. Neurol. 200, 430-437.
29. Nadrigny, F., Rivals, I., Hirrlinger, P., Koulakoff, A., Personnaz, L., Vernet, M., Allioux, M., Chameil, M., Ropert, N., Giaume, C., et al. (2006). Detecting fluorescent protein expression and colocalization on single secretory vesicles with linear spectral unmixing. Eur. Biophys. J. 35, 533-547.
30. Ohad, N., Shichrur, K., and Yalovsky, S. (2007). The analysis of protein- protein interactions in plants by bimolecular fluorescence complementation. Plant Physiol. 145, 1090-1099.
31. Pakhomov, A.A., Martynova, N.Y., Gurskaya, N.G., Balashova, T.A., and Martynov, V.I. (2004). Photoconversion of the chromophore of a fluorescent protein from Dendronephthya sp. Biochem. (Mosc.). 69, 901-908.
32. Patterson, G.H., Piston, D.W., and Barisas, B.G. (2000). Förster distances between green fluorescent protein pairs. Anal. Biochem. 284, 438-440.
33. Pisharath, H., Rhee, J.M., Swanson, M.A., Leach, S.D., and Parsons, M.J. (2007). Targeted ablation of beta cells in the embryonic zebrafish pancreas using E. coli nitroreductase. Mech. Dev. 124, 218-229.
34. Pulido, P., Spínola, M.C., Kirchsteiger, K., Guinea, M., Pascual, M.B., Sahrawy, M., Sandalio, L.M., Dietz, K.J., González, M., and Cejudo, F.J. (2010). Functional analysis of the pathways for 2-Cys peroxiredoxin reduction in Arabidopsis thaliana chloroplasts. J. Exp. Bot. 61, 4043-4054.
35. Raab-Graham, K.F., Haddick, P.C., Jan, Y.N., and Jan, L.Y. (2006). Activity and mTor-dependent suppression of Kv1.1 channel mRNA translation in dendrites. Science. 314, 144-148.
36. Schäfer, S.P., Dittrich, P.S., Petrov, E.P., and Schwille, P. (2006). Single molecule fluorescence imaging of the photoinduced conversion and bleaching behavior of the fluorescent protein Kaede. Microsc. Res. Tech. 69, 210-219.
37. Schleifenbaum, F., Blum, C., Elgass, K., Subramaniam, V., and Meixner, A.J. (2008). New insight into the photophysics of DsRed by multiparameter spectroscopy on single proteins. J. Phys. Chem. B. 112, 7669-7674.
38. Schleifenbaum, F., Elgass, K. Sackrow, M., Caesar, K., Berendzen, K. Meixner, A.J., and Harter, K. (2010). Fluorescence intensity decay shape analysis microscopy (FIDSAM) for quantitative and sensitive live-cell imaging: a novel technique for fluorescence microscopy of endogenously expressed fusion-proteins. Mol. Plant. 3, 555-562.
39. Schmidt, A., Wiesner, B. Weisshart, K., Schulz, K., Furkert, J. Lamprecht, B., Rosenthal, W., and Schülein, R. (2009). Use of Kaede fusions to visualize recycling of G-protein-coupled receptors. Traffic. 10, 2-15.
40. Schnitzer, D., Seidel, T. Sander, T., Golldack, D., and Dietz, K.J. (2011). The cellular energization state affects peripheral stalk stability of plant vacuolar H+-ATPase and impairs vacuolar acidification. Plant Cell Physiol. 52, 946-956.
41. Scott, E.K., Mason, L., Arrenberg, A.B. Ziv, L., Gosse, N.J., Xiao, T., Chi, N.C., Asakawa, K., Kawakami, K., and Baier, H. (2007). Targeting neural circuitry in zebrafish using GAL4 enhancer trapping. Nat. Methods. 4, 323-326.
42. Seidel, T., Golldack, D., and Dietz, K.J. (2005). Mapping of C-termini of V-ATPase subunits by in vivo-FRET analysis. FEBS Lett. 579, 4374-4382.
43. Seidel, T., Kluge, C., Hanitzsch, M., Ross, J., Sauer, M., Dietz, K.J., and Golldack, D. (2004). Co-localization and FRET-analysis of subunits c and a of the vacuolar H+-ATPase in living plant cells. J. Biotechnol. 112, 165-175.
44. Seidel, T., Seefeldt, B., Sauer, M., and Dietz, K.J. (2010). In vivo analysis of the 2-Cys peroxiredoxin oligomeric state by twostep FRET. J. Biotechnol. 149, 272-279.
45. Stark, D.A., and Kulesa, P.M. (2007). An in vivo comparison of photoactivatable fluorescent proteins in an avian embryo model. Dev. Dyn. 236, 1583-1594.
46. Subach, O.M., Patterson, G.H., Ting, L.M., Wang, Y., Condeelis, J.S., and Verkhusha, W. (2011). A photoswitchable orangeto- far-red fluorescent protein, PSmOrange. Nat. Methods. 8, 771-777.
47. Tomura, M., Yoshida, N., Tanaka, J., Karasawa, S., Miwa, Y., Miyawaki, A., and Kanagawa, O. (2008). Monitoring cellular movement in vivo with photoconvertible fluorescence protein 'Kaede' transgenic mice. Proc. Natl Acad. Sci. U S A. 105, 10871-10876.
48. Tsutsui, H., Karasawa, S., Shimizu, H., Nukina, N., and Miyawaki, A. (2005). Semi-rational engineering of a coral fluorescent protein into an efficient highlighter. EMBO Rep. 6, 233-238.
49. Uemura, T., Ueda, T., Ohniwa, R.L., Nakano, A., Takeyasu, K., and Sato, M.H. (2004). Systematic analysis of SNARE molecules in Arabidopsis: dissection of the post-Golgi network in plant cells. Cell. Struct. Funct. 29, 49-65.
50. Vogelaar, C.F., Gervasi, N.M., Gumy, L.F., Story, D.J., Raha- Chowdhury, R., Leung, K.M., Holt, C.E., and Fawcett, J.W. (2009). Axonal mRNAs: characterization and role in the growth and regeneration of dorsal root ganglion axons and growth cones. Mol. Cell. Neurosci. 42, 102-115.
51. Watanabe, W., Shimada, T., Matsunaga, S., Kurihara, D., Fukui, K., Arimura, S., Tsutsumi, N., Isobe, K., and Itoh, K. (2007). Singleorganelle tracking by two-photon conversion. Opt. Express. 15, 2490-2498.
52. Woolfe, F., Gerdes, M., Bello, M., Tao, X., and Can, A. (2011). Autofluorescence removal by non-negative matrix factorization. IEEE Transact. Image Process. 20, 1085-1093.