| | | | | | | |
71. Kim, J., Rudella, A., Ramirez-Rodriguez, V., Zybailov, B., Olinares, PDB, van Wijk, K.J. (2009) Subunits of the plastid ClpPR protease complex have differential contributions to embryogenesis, plastid biogenesis, and plant development in Arabidopsis. Plant Cell Jun 12. [Epub ahead of print]
70. Zybailov, B., Friso, G., Kim, J., Rudella, A., Ramirez-Rodriguez, V., Asakura, Y, Sun, Q., , van Wijk, K.J. (2009) Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis and feedback regulation of metabolism. Mol Cell Proteomics. (prepublication on-line May 7)
69. Kroeger TS, Watkins KP, Friso G, van Wijk KJ, Barkan A.(2009) A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing. Proc Natl Acad Sci U S A. 106(11):4537-42
68. Majeran, W. and van Wijk, K.J. (2009) Cell-type specific differentiation of chloroplasts in C4 plants. Trends Plant Sci. 14(2):100-9.
67. Sun, Q,, Zybailov, B., Majeran, W., Friso, G., Olinares, P.D.B., van Wijk, K.J. (2008) PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res. 37: D969-74
66. Wagner, S., Klepsch, M.M., Schlegel, S., Appel, A., Draheim, R., Tarry, M., Högbom, M., van Wijk, K.J., Slotboom, D.J., Persson, J.O., de Gier, J.W. (2008) Tuning Escherichia coli for membrane protein overexpression. Proc Natl Acad Sci U S A. 105(38):14371-6
65. Prikryl J, Watkins KP, Friso G, Wijk KJ, Barkan A. (2008) A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis. Nucleic Acids Res. 36(16):5152-65
64. Klepsch M, Schlegel S, Wickström D, Friso G, van Wijk KJ, Persson JO, de Gier JW, Wagner S. (2008) Immobilization of the first dimension in 2D blue native/SDS-PAGE allows the relative quantification of membrane proteomes. Methods. Jul 29, 2008
63. Rutschow H, Ytterberg AJ, Friso G, Nilsson R, van Wijk KJ. (2008) Quantitative proteomics of a chloroplast SRP54 sorting mutant and its genetic interactions with CLPC1 in Arabidopsis thaliana. Plant Physiol.. 148(1):156-75
62. Majeran W, Zybailov B, Ytterberg AJ, Dunsmore J, Sun Q, van Wijk KJ. (2008) Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells. Mol Cell Proteomics. 7(9):1609-38
61. Zybailov B, Rutschow H, Friso G, Rudella A, Emanuelsson O, Sun Q, van Wijk KJ. (2008) Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS ONE. Apr 23;3(4)
60. Covshoff, S., Majeran, W., Liu, P., Kolkman, J.M., van Wijk, K.J., Brutnell, T.P.(2008) De-regulation of maize C4 photosynthetic development in a mesophyll cell defective mutant. Plant Physiol. 146(4):1469-81
59. Baars, L., Wagner, S.,Wickström, D., Klepsch, M., Ytterberg, A.Y., van Wijk, K.J., de Gier, J.W. (2008) Effects of SecE depletion on the inner and outer membrane proteomes of Escherichia coli. J. Bacteriology. 190(10):3505-25
58. Giacomelli, L., Masi, A., Ripoll, D.R., Lee, M.J., van Wijk, K.J. (2007) Arabidopsis thaliana deficient in two chloroplast ascorbate peroxidases shows accelerated light-induced necrosis when levels of cellular ascorbate are low. Plant Molecular Biology 65(5):627-44
57. Watkins, K.P, Kroeger, T.S, Cooke, A.M, Williams-Carrier, R.E., Friso, G., Belcher, S.E., van Wijk, K.J., Barkan, A. (2007). A Ribonuclease III Domain Protein Functions in Group II Intron Splicing in Maize Chloroplasts. The Plant Cell 19(8):2606-23
56. Brehelin, C., Kessler, F., van Wijk, K.J. (2007) Plastoglobules: versatile lipoprotein particles in plastids. Trends in Plant Science 12(6):260-6
55. Wagner, S., Baars, L., Ytterberg, A.J., Klussmeier, A., Wagner, C.S., Nord, O., Nygren, PA, van Wijk, K.J., de Gier, J.W. (2007) Consequences of membrane overexpression in Escheria coli. Molecular Cellular Proteomics 6(9):1527-50
54. Schoonheim, P.J., Veiga, H., da Costa Pereira, D., Friso, G., van Wijk, K.J. de Boer, A.H. (2007) A comprehensive analysis of the 14-3-3 interactome in barley leaves using a complementary proteomics and two-hybrid approach. Plant Physiology 143(2):670-83
53. Nissinen, R.M., Ytterberg, A.Y., Bogdanove, A.J., van Wijk, K.J. and Beer, S.V. (2007) Analyses of the secretomes of Erwinia amylovora and selected hrp mutants reveal novel type III secreted proteins and an effect of HrpJ on extracellular harpin levels. Molecular Plant Pathology 8, 55-67
52. Rudella, A., Friso, G., Alonso, J.M., Ecker, J.R., van Wijk, K.J. (2006) Down-regulation of ClpR2 protease of A. thaliana leads to reduced accumulation of the ClpPRS complex and defects in chloroplast biogenesis. The Plant Cell 18(7), 1704-1721
51. Giacomelli, L., Andrea Rudella, A. and van Wijk, K.J. (2006). High light response of the thylakoid proteome in Arabidopsis thaliana wild type and the ascorbate deficient mutant vtc2-2; a comparative proteomics study. Plant Physiology 141(2), 685-701
50. van Wijk, K.J. Peltier, J.B., Giacomelli, L. (2006) Isolation of chloroplast proteins from Arabidopsis thaliana for proteome analysis. Methods Molecular Biology 355:43-8
49. Adam, Z., Rudella, A., van Wijk, K.J. (2006) Recent advances in the study of Clp, FtsH and other proteases located in chloroplasts. Current Opinion in Plant Biology 9 (3), 234-40
48. Ytterberg A.J., Peltier, J.B., van Wijk, K.J. (2006) Protein profiling of plastoglobules in chloroplasts and chromoplasts; a surprising site for differential accumulation of metabolic enzymes. Plant Physiology 140, 984-997.
47. Zabrouskov, V., Han, X., Welker,E., Zhai, H., Lin, C., van Wijk, K., Scheraga, H.A., McLafferty., F.W. (2006) Stepwise Deamidation of Ribonuclease A at Five Sites Determined by Top Down Mass Spectrometry. Biochemistry 45, 987-992
46. Baars, L. Ytterberg, A.Y., Drew, D., Wagner, S., Thilo, C., van Wijk, K.J. and de Gier, J.W. (2005) Defining the role of the E. coli chaperone SECB using comparative proteomics. J. Biol. Chem 281, 10024-10034
45. Majeran, W., Cai, Y., Sun, Q., van Wijk, K.J. (2005) Functional differentiation of Bundle Sheath and Mesophyll maize chloroplasts determined by Comparative proteomics. Plant Cell 17(11) 3111-40
44. Majeran, W., Friso, G., van Wijk, K.J., Vallon, O. (2005) The chloroplast ClpP complex in Chlamydomonas reinhardtii contains an unusual high molecular mass subunit with a large apical domain. FEBS J. 272(21),5558-5571.
43. Peltier, J.B., Cai, Y., Sun, Q., Zabrouskov, V., Giacomelli, L., Rudella, A., Ytterberg, AJ, Rutschow, H., van Wijk, K.J. (2006) The oligomeric stromal proteome of A. thaliana chloroplasts. Mol. Cell Proteomics 5(1):114-33. Oct 4 Epub
42. van Wijk, K.J. (2005) Expression, Prediction and Function of the thylakoid proteome in higher plants and green algae. In "The Structure and Function of Plastids", edited by RR. Wise and JK Hoober. Volume 13 of Series on Advances in Photosynthesis and Respiration. Series editor Gonvidjee. Kluwer Academic Publishers (in Press)
41. Drew D, Slotboom DJ, Friso G, Reda T, Genevaux P, Rapp M, Meindl-Beinker NM, Lambert W, Lerch M, Daley DO, Van Wijk KJ, Hirst J, Kunji E, De Gier JW.A (2005) A scalable, GFP-based pipeline for membrane protein overexpression screening and purification. Protein Sci. 14(8), 2011-2017
40. van Wijk, KJ. (2004) Plastid Proteomics. Plant Physiology and Biochemistry 42(12):963-77
39. Labate, M.T. V., Ko, K., Ko, Z.W., Costa Pinto, L.S.R., Real, M.J.U.D., Romano, M.,Barja, P.R., Granell, A.,Friso, G., van Wijk, K.J., and Labate, C.A. (2004) Constitutive expression of pea LHCb1.2 in tobacco affects plant development, morphology and photosynthetic capacity. Plant Molecular Biology 55, 701-714
38. Peltier, J-B, Ytterberg, A.J., Sun, Q. and van Wijk, K.J. (2004) New functions of the thylakoid membrane proteome of Arabidopsis thaliana revealed by a simple, fast and versatile fractionation strategy. J. Biol. Chemistry 279, 49367-49383
37. Suzuki, J.Y, Ytterberg, A.Y., Beardslee, T.A., Allison, L.A., van Wijk, K.J. and Maliga, P. (2004) Affinity purification of the tobacco plastid RNA polymerase and in vitro reconstitution of the holoenzyme. Plant Journal Oct 40(1):164-72
36. Sun, Q., Emanuelsson, O., van Wijk, K.J. (2004) Analysis of curated and predicted plastid subproteomes of Arabidopsis. Subcellular compartmentalization leads to distinctive proteome properties. Plant Physiology 15, 723-734
35. Friso*, G., Giacomelli*, L., Ytterberg*, A.J., Peltier*, J.B., Rudella, A. Sun, Q., van Wijk, K.J. (2004) In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts; new proteins, new functions and a plastid proteome database. Plant Cell 16, 478-499 (*contributed equally)
34. van Wijk, K.J. (2003) Chloroplast Proteomics. In "Plant Functional Genomics", The Haworth's Food Products Press, Binghamton, New York. pp. 329-358
33. Peltier*, J.B, Ripoll*, D, Friso, G. Rudella, A.,, Ytterberg, J., Cai, Y., Giacomelli, L., Pillardy, J and van Wijk (2004) . Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted 3-D structures and functional implications. J. Biol. Chemistry 279, 4768 - 4781 (*contributed equally)
32. Zabrouskov,V., Giacomelli, L., van Wijk,K.J., and McLafferty, F.W. (2003) A new mass spectrometry approach for Plant proteomics: characterization of chloroplast proteins of Arabidopsis thaliana by top down mass spectrometry. Molecular and Cellular Proteomics 2.12, 1253-1260
31. Tregoning, J.S., Nixon, P., Kuroda, H., Svab, Z., Clare, S., Bowe, F., Fairweather, N., Ytterberg, J., van Wijk, K.J., Dougan, G., Maliga, P. (2003) Expression of tetanus toxin fragment C in tobacco chloroplasts. Nucleic acids Research 31 (4) 1174-1179
30. Nilsson, R. and van Wijk, K.J. (2002) Transient interaction of cpSRP54 with elongating nascent chains of the chloroplast-encoded D1 protein; ‘cpSRP54 caught in the act’. FEBS letters 524, 127-133
29. Jiang, F., Yi, L., Moore, M., Rohl, T., van Wijk, K.J., de Gier, J.W., Henry, R., and Dalbey, R. (2002) Chloroplast Oxa1p Homologue Albino3 Can Functionally Complement the Bacterial YidC Depletion Strain and Promote Membrane Insertion of Both Bacterial and Chloroplast Thylakoid Proteins. J. Biol. Chemistry 277, 19281-19288
28. Peltier, J-B., Emanuelsson, O., Kaluma, D.E., Ytterberg, J., Friso, G., Rudella, A., Liberles, D.A., Soderberg, L., Roepstorff, P., von Heijne, G. and van Wijk, K.J. (2002) Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction. Plant Cell 14, 211-236
27. van Wijk, K.J. (2001) Proteins involved in Biogenesis of the thylakoid membrane In: Advances in Photosynthesis "Regulatory aspects of Photosynthesis, (Aro and Andersson and eds). Volume 8. Kluwer Academic Publishers. pp.153-175
26. Röhl, T. and van Wijk, K.J. (2001) In vitro Reconstitution of Insertion and Processing of Cytochrome f in a Homologous Chloroplast Translation System. J. Biol. Chemistry 276, 35465-35472
25. Fröderberg, L., Röhl, T., van Wijk, K.J. and de Gier, J.W. (2001) Complementation of bacterial SecE by a chloroplastic homologue. FEBS Letters 498, 52-56
24. van Wijk, K.J. (2001) Update on plant proteomics. Challenges and Prospects of Plant Proteomics. Plant Physiology 126, 501-508
23. Peltier, J.B., Ytterberg, J., Lieberles, D., Roepstorff, P. and van Wijk, K.J. (2001) Identification of a 350 kDa chloroplast ClpP protease complex by BN-PAGE and Mass spectrometry. J. Biol. Chemistry 276: 16318-16327
22. van Wijk, K.J. (2000) Proteomics of the chloroplast; Experimentation and prediction. Trends in Plant Science 5, 420-425
21. Zhang, L., Paakkarinen,V., van Wijk, K.J. and Aro, E-M. (2000) Biogenesis of the chloroplast-encoded D1 protein: Regulation of mechanisms of D1 protein translation elongation, insertion and assembly. Plant Cell 12, 1769-1781
20. Peltier, J.-B., Friso, G., Kalume, D.E., Roepstorff, P., Nilsson, F., Adamska, I. and van Wijk, K.J. (2000) Proteomics of the chloroplast: Systematic identification and targeting analysis of thylakoid proteins. Plant Cell 12, 319-341
19. Zhang, L., Paakkarinen, V., van Wijk, K.J. and Aro, E-M. (1999). Co-translational assembly of the D1 protein into Photosystem II complexes. J. Biol. Chemistry. 274, 16062-16067
18. Houben, E., de Gier, J.W. and van Wijk, K.J. (1999). Insertion of leader peptidase into the thylakoid membrane during synthesis in a chloroplast translation system. Plant Cell 11, 1553-1564
17. Nilsson, R., Brunner, J., Hoffman, N. and van Wijk, K. J. (1999). Interactions of ribosome nascent chain complexes of the chloroplast-encoded D1 thylakoid membrane protein with cpSRP54. EMBO J. 18(3), 733-742
16. Pilgrim, M., van Wijk, K.J., Parry, D.H., Sy, D.A.C. and Hoffman, N. (1998) Expression of a dominant negative form of SRP54 inhibits chloroplast biogenesis in Arabidopsis thaliana. Plant Journal 13, 177-186
15. Kettunen, R., Salli, S., Rintamaki, E., van Wijk, K.J. and Aro, E-M. (1997) PsbA gene expression in pea leaves during high light stress and subsequent recovery. Eur. J Biochemistry 247, 441-448
14. van Wijk, K.J., Roobol-Boza, M., Kettunen, R., Andersson, B. and Aro, E-M. (1997) Synthesis and assembly of the D1 protein into Photosystem II; Processing of the C-terminus and identification of initial assembly partners and complexes during Photosystem II repair. Biochemistry 36, 6178-6168
13. van Wijk, K.J. and Eichacker, L. (1996) Light triggers release of polysome bound D1 protein and integration into Photosystem II. FEBS Letters. 388, 89-93
12. van Wijk, K.J., Andersson, B., and Aro, E-M. (1996) Kinetic resolution of the incorporation of the D1 protein into PSII and localization of assembly intermediates in thylakoid membranes of spinach chloroplasts. J. Biol. Chemistry. 271, 9627-9636
11. van Wijk, K.J., Bingsmark, S., Aro, E-M. and Andersson, B. (1995) In vitro synthesis and incorporation of PSII core proteins: the D1 protein can be incorporated into Photosystem II in isolated chloroplasts and thylakoids. J. Biol. Chemistry. 270, 25685-25696
10. van Wijk, K.J., Knott, T. and Robinson, C. (1995) Evidence for Sec A and ΔpH independent insertion of D1 into thylakoids. FEBS Letters. 368, 263-266
9. van Wijk, K.J., Nilsson, L.O. and Styring, S. (1994) Synthesis of reaction centre proteins and reactivation of redox components during repair of photosystem II after light-induced inactivation. J. Biol. Chemistry. 269, 28382-28392
8. Roffey, R.A., van Wijk, K.J., Sayre, R.T. and Styring, S. (1994) Spectroscopic characterization of TyrZ in histidine 190 mutants of the D1-protein in photosystem II in Chlamydomonas reinharditii: Implications for the structural model of the donor side of PSII. J. Biol. Chemistry. 269, 5115-5121
7. van Wijk, K.J. and van Hasselt, P.R. (1993) Kinetic resolution of different recovery phases of photoinhibited Photosystem II in cold-acclimated and non-acclimated spinach leaves. Physiol. Plantarum 87, 187-183
6. van Wijk, K.J. and van Hasselt, P.R. (1993) Photoinhibition of Photosystem II in vivo is preceded by down-regulation through light-induced acidification of the lumen; Consequences for the mechanism of photoinhibition in vivo. Planta 189, 359-368
5. van Wijk, K.J., Schnettger, B., Graf, M. and Krause, G.H. (1993) Photoinhibition and recovery of Photosystem II in relation to heterogeneity. Biochim. Biophys. Acta (Biomembranes) 1142, 59-68
4. van Wijk, K.J., Andersson, B. and Styring, S. (1992) Spectroscopic characterization of photoinhibited photosystem II and kinetic resolution of the triggering of the D 1-reaction center protein for degradation. Biochim. Biophys. Acta (Biomembranes) 1100, 207-215
3. van Wijk, K.J. and Krause, G.H. (1991) O2 dependence of photoinhibition at low temperatures in intact protoplast of Valerianella locusta L. Planta 186, 135-142
2. van Wijk, K.J. and van Hasselt, P.R. (1990) The quantum efficiency of photosystem II and its relation to non-photochemical quenching of chlorophyll fluorescence as affected by temperature and light intensity; a comparison of methods. Photosynth. Res. 25, 233-240
1. van Hove, L.W.A., van Kooten, O., van Wijk, K.J., Vredenberg, W.J., Adema, E.H. and Pieters, E.A. (1990) Physiological effects of long term exposure to low concentrations of SO2 and NH3 on poplar leaves. Physiol. Plantarum 82, 32-40
10. Houben, E., Nilsson, R., de Gier, J.W., Brunner, J., Hoffman, N.E. and van Wijk, K.J. (1999) Reconstitution of co-translational targeting of polytopic membrane proteins to the thylakoids in a homologous chloroplast translation system. In: NATO advanced research workshop. The Chloroplast; From Molecular Biology to Biotechnology. (Dr. J. Argyroudi-Akoyunoglou and H. Senger, eds.), 327-342
9. Zhang, L-X., van Wijk, K.J. and Aro, E.M. (1998) Co-translational insertion of the D1 protein into Photosystem II during repair. In: Proceedings XIth International Congress on Photosynthesis (Drs. G. Garab, ed) Vol IV, 3127-3130
8. van Wijk, K.J., Nilsson, R., Houben, E., Brunner, J. and Hoffman, N.E. (1998) Co-translational interaction of cpSRP54 to nascent chains of the chloroplast encoded D1 protein probed in a homologous chloroplast translation system. In: Proceedings XIth International Congress on Photosynthesis (Drs. G. Garab ed.) Vol IV, 3123-3126
7. Houben, E., de Gier, J.W. and van Wijk, K.J. (1998) Co-translational targeting of leader peptidase to the thylakoid membrane; reconstitution in a homologous chloroplast translation system. In: Proceedings XIth International Congress on Photosynthesis (Drs. G. Garab, ed) Vol. IV, 3119-3122
6. van Wijk, K.J., Andersson, B. and Aro, E-M. (1995) Mechanism of replacement of the D1 protein in Photosystem II and localization of assembly intermediates. In: Photosynthesis: from Light to Biosphere (Mathis, P., ed.). Kluwer. Dordrecht, The Netherlands. Vol. III, 823-826
5. van Wijk, K.J., Bingsmark, S., Aro, E-M. and Andersson, B. (1995) Synthesis and assembly of the D1 protein in isolated thylakoids and chloroplasts. In: Photosynthesis: from Light to Biosphere (Mathis, P., ed.). Kluwer. Dordrecht, The Netherlands. Vol. III, 819-822
4. van Wijk, K.J. (1992) Photoinhibition of photosynthesis in higher plants. From photosystem II particle to intact leaf. Doctoral Thesis, Groningen, The Netherlands
3. van Wijk, K.J. and van Hasselt, P.R. (1992) Photoinhibition of Photosystem II in vivo: Does photoinhibition take place in the centers down-regulated by acidification of the lumen. In: Current Research in Photosynthesis (Murata, ed.) IV, 447-450, Dordrecht, The Netherlands
2. van Wijk, K.J. and van Hasselt, P.R. (1990) Effect of cold-hardening on the quantum yield of spinach leaves. In: Current Research in photosynthesis (Baltscheffski, ed.,) Vol. IV, 389-392, Elsevier, Dordrecht, The Netherlands
1. van Kooten, O., van Hove, B. and van Wijk, K.J. (1988) The effect of long term exposition of poplars to low concentrations of SO2 and NH3. In: Applications of Chlorophyll fluorescence (H.K. Lichtenthaler, ed.), 203-209. Kluwer Academic Publishers
 |
Klaas Jan van Wijk Department of Plant Biology, Emerson Hall Cornell University Ithaca NY 14853 kv35@cornell.edu |