Publications

Reviewed Publications
  1. Majsec, K., Bhuiyan, N., Sun, Q., Kumari, S., Kumar, V., Ware, D., van Wijk, K.J. (2017) The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis. The Plant Cell

  2. Bhuiyan, N.H and van Wijk, K.J. (2017) Functions and substrates of plastoglobule-localized metallopeptidase PGM48. Plant Signalling and Behavior 12(6):e1331197.

  3. Davis, L.R., Klonoski,K., Rutschow,H.L., van Wijk, K.J., Sun, Q., Haribal, M.M., Saporito, R.A. Vega, A., Rosenblum, E.B., Zamudio,K.R., Robertson, J.M. (2016) Host Defense Skin Peptides Vary with Color Pattern in the Highly Polymorphic Red-Eyed Treefrog. Frontiers in Ecology and Evolution 4:97 doi: 10.3389/fevo.2016.00097

  4. van Wijk, K. J. and Kessler, F. (2017) Plastoglobuli are plastid micro-compartments with integrated functions in metabolism, plastid developmental transitions and environmental adaptation. Annual Review in Plant Biology 68, 253-289

  5. Bhuiyan, N.H., Friso, G., Rowland, E., Majsec, K., van Wijk, K.J. (2016) Plastoglobule localized metallopeptidase PGM48 is a positive regulator of seneescence in Arabidopsis thaliana. The Plant Cell 28(12):3020-3037

  6. Lohscheider, J.N., Friso, G. and van Wijk, KJ. (2016) Phosphorylation of plastoglobular proteins in Arabidopsis thaliana. J. Exp Botany 67(13):3975-84

  7. Apitz, J., Nishimura, K., Schmied, J., Wolf, A., Hedtke, B., van Wijk, K.J., Grimm, B. (2016) Post-translational control of ALA synthesis includes GluTR degradation by Clp protease and stabilisation of GluTR-biding protein. Plant Physiology 170(4):2040-51

  8. Rowland,E., Kim, J., Bhuiyan, N.H., van Wijk, K.J. (2015) The Arabidopsis Chloroplast stromal N-terminome; complexities of N-terminal protein maturation and stability. Plant Physiology 169, 1881-1896

  9. Friso and van Wijk (2015) Update: Post-translational protein modifications in Plant Metabolism. Plant Physiology 169, 1469-1487

  10. Nishimura, K., Apitz, J., Friso, G., Kim, J., Ponnala, L., Grimm, B., van Wijk, K.J. (2015) Discovery of a unique Clp component, ClpF, in chloroplasts: a proposed binary ClpF-ClpS1 adaptor complex functions in substrate recognition and delivery. Plant Cell 10, 2677-2691

  11. Ort et al. (2015) Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proc Natl Acad Sci U S A. 112(28):8529-36

  12. Kim, J., Kimber, M.S., Nishimura, K., Friso, G., Schultz, L., Ponnala, L., van Wijk, K.J. (2015) Structures, Functions, and Interactions of ClpT1 and ClpT2 in the Clp Protease System of Arabidopsis Chloroplasts. Plant Cell 27(5):1477-96

  13. Offermann, S., Friso, G., Kelly, A., Doroshenk, K.A., Sun,Q., Sharpe, R.M., Okita, T.W., Edwards, G.E., van Wijk, K.J. (2015) Development and subcellular organization of single-cell C4 photosynthesis in Bienertia sinuspersici determined by large scale proteomics and cDNA assembly from 454 DNA sequencing. J. Proteome Research 14(5):2090-108

  14. Sun, T., Shi, X., Friso, G., van Wijk, K.J., Bentolila, S., Hanson, M.R. (2015) A zinc finger motif-containing protein is essential for chloroplast RNA editing. PlosGenetics 11(3) :e1005028

  15. Manohar M, Tian M, Moreau M, Park SW, Choi HW, Fei Z, Friso G, Asif M, Manosalva P, von Dahl CC, Shi K, Ma S, Dinesh-Kumar SP, O'Doherty I, Schroeder FC, van Wijk KJ, Klessig DF (2015) Identification of multiple salicylic acid-binding proteins using two high throughput screens. Front Plant Sci. 2015 Jan 12;5:777

  16. Tian. M., Sasvani, Z., Gonzalez, P.A., Friso, G., Rowland, E., Liu, X.M., van Wijk, K.J., Nagy, PD., Klessig, D. (2015) Salicylic acid inhibits the replication of Tomato Bushy Stunt Virus by directly targeting a host component in the replication complex. Mol Plant Microbe Interact. 2015 28(4):379-86

  17. van Wijk (2015) Protein Maturation and Proteolysis in plant plastids, mitochondria and peroxisomes. Annual Review in Plant Biology 66:75-111

  18. Bhuiyan, N.H., Friso, G., Poliakov, A., van Wijk, K.J. (2015) MET1 is a thylakoid-associated TPR protein involved in photosystem II supercomplex formation and repair. Plant Cell 27(1):262-85

  19. Nishimura, K and van Wijk, K.J. (2015) The Clp protease system in non-green plastids and chloroplasts. BBA invited review 1847(9):915-30

  20. Tapken, W., Kim, J., van Wijk, K.J., Pilon, M. (2015) The Clp protease system is required for copper ion-dependent turnover of the PAA2/HMA8 copper transporter in chloroplasts. New Phytologist 205(2):511-7.

  21. Russell, C.W., Poliakov, A., Haribal, M., Jander, G., van Wijk, K.J., Douglas, A.E. (2014) Matching the Supply of Bacterial Nutrients to the Nutritional Demand of the Animal Host. Proc Biol Sci. 2014 Sep 22;281(1791)

  22. van Wijk, K.J. Friso, G., Walther, D., Schulze, W.X. (2014) Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifs. Plant Cell 26(6):2367-2389

  23. Ponnala L., Wang Y., Sun Q., van Wijk K.J (2014) Correlation of mRNA and protein abundance in the developing maize leaf. Plant Journal 78(3):424-40

  24. Nishimura, K., Asakura, Y., Friso, G., Kim, J., Oh, H, Rutschow, H., Ponnala, L., van Wijk, K.J. (2013) ClpS1 is a conserved substrate selector for the chloroplast Clp protease system in Arabidopsis thaliana. Plant Cell 25(6):2276-301

  25. Lundquist P.K., Poliakov A., Giacomelli L., Friso G., Appel M., McQuinn R.P., Krasnoff S.B., Rowland E., Ponnala L., Sun Q., van Wijk K.J. (2013) Loss of plastoglobule kinases ABC1K1 and ABC1K3 leads to conditional degreening, modified prenyl-lipids and recruitment of the JA pathway. Plant Cell 25(5):1818-39

  26. Kim J., Olinares P.D., Oh S.H., Ghisaura S., Poliakov A., Ponnala L, van Wijk K.J. (2013) Modified Clp Protease Complex in the ClpP3 Null Mutant and Consequences for Chloroplast Development and Function in Arabidopsis. Plant Physiol. 2013 May;162(1):157-79

  27. Huang, M., Friso, G., Nishimura, K., Qu, X., Olinares, P.D.B., Majeran, W., Sun, Q., van Wijk, K.J. (2012) Construction of plastid reference proteomes for maize and Arabidopsis and evaluation of their orthologous relationships; the concept of orthoproteomics. Journal of Proteomics Research 12(1):491-504

  28. Tian M, von Dahl CC, Liu PP, Friso G, van Wijk KJ, Klessig DF.(2012) The combined use of photoaffinity labeling and surface plasmon resonance-based technology identifies multiple salicylic acid-binding proteins. Plant J. 72(6):1027-38

  29. Derrien, B., Majeran, W., Effantin, G., Ebenezer, J., Friso, G., van Wijk, K.J., Steven, A.C. , Maurizi, M.R., and Vallon, O. (2012) The Purification of the Chlamydomonas reinhardtii chloroplast ClpP complex: additional subunits, domains and structural features. Plant Molecular Biology 80(2):189-202.

  30. Lundquist, P.K., Davis, J.I., and. van Wijk, K.J. (2012) ABC1K atypical kinases in photosynthetic organisms; filling the organellar kinase void. Trends in Plant Science. Trends in Plant Science 17(9):546-55

  31. Asakura, Y., Galarneau, E, Watkins, K.P., Barkan, A., van Wijk, K.J. (2012) Chloroplast RH3 DEAD-box RNA helicases in Zea mays and Arabidopsis thaliana function in splicing of specific group II introns and affect chloroplast ribosome biogenesis. Plant Physiology. Plant Physiology 159 (3), 961-974

  32. Bentolila, S., Heller, W.P., Sun, T., Babina, A.M., Friso,G., van Wijk, K.J., and Hanson, M.R. (2012) RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Proc Natl Acad Sci U.S.A. Proc Natl Acad Sci U.S.A. 109(22), E1453-1461

  33. Lundquist, P.K., Poliakov, A., Bhuiyan N.H., Zybailov, B., Sun, Q., van Wijk, K.J. (2012) The functional network of the Arabidopsis thaliana plastoglobule proteome based on quantitative proteomics and genome-wide co-expression analysis. Plant Physiology 158(3) 1172-1192

  34. Majeran, W., Friso, G., Asakura, Y., Qu, X., Huang, M., Ponnala, L., Kenneth P. Watkins, K.P., Barkan, A., van Wijk, K.J. (2012) Nucleoid-enriched proteomes in developing plastids and chloroplasts from maize leaves; a new conceptual framework for nucleoid functions. Plant Physiology 158(1):156-189

  35. Klaas J. van Wijk (2011) Plant Proteomics and Photosynthesis. Chapter 7, pp 151-173. In "Photosynthesis: Plastid Bioklogy, Energy Conversion and Carbon Assimilation" edited by JJ. Eaton-Rye, B.C. Tripathy and T.D. Sharkey. Volume 34 of Series on Advances in Photosynthesis and Respiration. Series editor Gonvidjee. Kluwer Academic Publishers.

  36. Lee, J-Y.,Wang, X., Cui, W., Sager, R., Modla, S. Kirk Czymmek, K., Zybailov, B., van Wijk, K.J., Zhang, C., Lu, H., Lakshmanan, V. (2011) A plasmodesmata-localized protein mediates a crosstalk between cell-to-cell communication and innate immunity in Arabidopsis The Plant Cell 23(9):3353-73

  37. Olinares, P.D.B, Kim, J., Davis, J.I. and van Wijk, K.J. (2011) Subunit stoichiometry, evolution and functional implications of an asymmetric plant plastid ClpP/R protease complex in Arabidopsis. The Plant Cell 23(6):2348-61

  38. Wickström D, Wagner S, Simonsson P, Pop O, Baars L, Ytterberg AJ, van Wijk KJ, Luirink J, de Gier JW. (2011) Characterization of the Consequences of YidC Depletion on the Inner Membrane Proteome of E. coli Using 2D Blue Native/SDS-PAGE. J Mol Biol. 3;409(2):124-35.

  39. Agrawal, G.K., Job, D., Zivy, M., Agrawal, V.P., Bradshaw, R.A., Dunn, M.J., Haynes, P.A., van Wijk, K.J., Kikuchi, S., Renaut, J., Weckwerth, W., Rakwal, R. (2011) Time to articulate a vision for the future of plant proteomics - A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO). Proteomics 11(9) 1559-1568

  40. Poliakov, A., Russell, C.W., Ponnala, L., Hoops, H.J., Sun, Q., Douglas, A.E., van Wijk, K.J. (2011) Large-Scale Label-Free Quantitative Proteomics of the Pea aphid-Buchnera Symbiosis. Molec. Cell Proteomics 10(6):M110.007039

  41. Watkins, K.P., Rojas, M., Friso, G., van Wijk, KJ, Meurer, J. and Barkan, A. (2011) APO1 promotes the splicing of chloroplast group II introns and harbors a novel plant-specific RNA binding domain (submitted) APO1 promotes the splicing of chloroplast group II introns and harbors a novel plant-specific RNA binding domain. Plant Cell 23(3):1082-92

  42. van Wijk, K.J. and Baginsky, S. (2011) Update on Plastid Proteomics in higher plants; current state and future goals. Plant Physiology 155(4):1578-88

  43. Sean E. Weise, Klaas J. van Wijk and Thomas D. Sharkey (2011) The role of transitory starch in C3, CAM, and C4 metabolism and opportunities for engineering leaf starch accumulation. J. Exp. Botany 62(9):3109-18

  44. Olinares, P.D.B., Kim, J, Wijk, K.J. (2011) The Clp protease system; a central component of the chloroplast protease network. BBA Biomembranes 1807(8):999-1011

  45. Friso, G., Olinares, P.D.B., van Wijk, K.J. (2011) The workflow for quantitative proteome analysis of chloroplast development and differentiation, chloroplast mutants, and protein interactions by spectral counting. Methods in Molecular Biology 775:265-82

  46. Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Shulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL. (2010) MASCP Gator: An aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol. 155(1):259-70

  47. Wickstrom, D., Wagner, S., Baars, L., Ytterberg, A.J., Klepsch, M., van Wijk, K.J., Luirink, J., de Gier, J.W. (2010) Consequences of depletion of the signal recognition particle in Escherichia coli. J Biol Chem. 286(6):4598-609

  48. Majeran, W., Friso, G, Ponnala, L., Connolly, B., Huang, M., Reidel, E., Zhang, C., Asakura, Y., Bhuiyan, N.H., Sun, Q., Turgeon, R., Wijk, K.J. (2010) Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics. The Plant Cell – 22(11):3509-42

  49. Olinares, P.D.B, L. Ponnala L., van Wijk, K.J. (2010) Megadalton Complexes in the Chloroplast Stroma of Arabidopsis thaliana characterized by Size Exclusion Chromatography, Mass Spectrometry and Hierarchical Clustering. Mol Cell Proteomics 9(7):1594-615

  50. Friso, G, Majeran, W., Huang, M., Sun, Q., van Wijk., K.J. (2010) Reconstruction of metabolic pathways, protein expression and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts; large scale quantitative proteomics using the first maize genome assembly. Plant Physiology 152:1219-1250

  51. Zybailov, B., Sun, Q., van Wijk, K.J. (2009) A Workflow for Large Scale Detection and Validation of Peptide Modifications by RPLC-LTQ-Orbitrap; application to the Arabidopsis thaliana leaf proteome and an on-line modified peptide library. Analytical Chemistry 81(19):8015-24

  52. 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 21(6):1669-1692

  53. 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 8(8): 1789-1810

  54. 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):4537-4542

  55. Majeran, W. and van Wijk, K.J. (2009) Cell-type specific differentiation of chloroplasts in C4 plants. Trends Plant Sci. 14(2):100-109

  56. 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-D974

  57. Wagner, S., Klepsch, M.M., Schlegel, S., Appel, A., Draheim, R., Tarry, M., Hogbom, 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):14371-14376

  58. 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):5152-5165

  59. Klepsch M, Schlegel S, Wickstrom 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 46(2):48-53

  60. 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):156-175

  61. 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):1609-1638

  62. 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 3(4):e1994

  63. 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):1469-1481

  64. Baars, L., Wagner, S.,Wickstrom, 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):3505-3525

  65. 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

  66. 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):2606-2623

  67. Brehelin, C., Kessler, F., van Wijk, K.J. (2007) Plastoglobules: versatile lipoprotein particles in plastids. Trends in Plant Science 12(6):260-266

  68. 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):1527-1550

  69. 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):670-683

  70. 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

  71. 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

  72. 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

  73. van Wijk, K.J. Peltier, J.B., Giacomelli, L. (2006) Isolation of chloroplast proteins from Arabidopsis thaliana for proteome analysis. Methods Molecular Biology 355:43-48

  74. 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), 234-240

  75. 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.
    Supplemental Table 1 | Supplemental Table 2.

  76. 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

  77. 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

  78. 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) 3111-3140
    Supplemental Table 1 | Supplemental Table 2 | Supplemental Table 3 | Supplemental Table 4

  79. 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

  80. 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):114-133
    Supplemental Table

  81. 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)

  82. 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

  83. van Wijk, KJ. (2004) Plastid Proteomics. Plant Physiology and Biochemistry 42(12):963-977

  84. 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

  85. 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
    Supplemental Table 1 | Supplemental Table 2

  86. 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 40(1):164-172

  87. 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
    Supplemental Table 1 | Supplemental Table 2 | Supplemental Table 3 | Supplemental Table 4 | Supplemental Figure 1 | Supplemental Figure 2

  88. 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 Cell16, 478-499 (*contributed equally)
    Supplemental Table 1 | Supplemental Table 2 | Supplemental Table 3

  89. van Wijk, K.J. (2003) Chloroplast Proteomics. In "Plant Functional Genomics", The Haworth's Food Products Press, Binghamton, New York. pp. 329-358

  90. 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)
    Supplemental Table 1 | Supplemental Table 2 | Supplemental Table 3 | Supplemental Table 4 | Clp homology models in PDB format | Clp homology models - 3D

  91. 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

  92. 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

  93. 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

  94. 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

  95. 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

  96. 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

  97. 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

  98. 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

  99. van Wijk, K.J. (2001) Update on plant proteomics. Challenges and Prospects of Plant Proteomics. Plant Physiology 126, 501-508

  100. 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

  101. van Wijk, K.J. (2000) Proteomics of the chloroplast; Experimentation and prediction. Trends in Plant Science 5, 420-425

  102. 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

  103. 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

  104. 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

  105. 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

  106. 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

  107. 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

  108. 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

  109. 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

  110. 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

  111. 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

  112. 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

  113. 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

  114. 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

  115. 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

  116. 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

  117. 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

  118. 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

  119. 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

  120. 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

  121. 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

  122. 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
Proceedings
  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. van Wijk, K.J. (1992) Photoinhibition of photosynthesis in higher plants. From photosystem II particle to intact leaf. Doctoral Thesis, Groningen, The Netherlands

  8. 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

  9. 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

  10. 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