Annis, M.Y., Ravenburg, C.M., van Wijk, K.J. (2024) Uvr motifs and their involvement in chloroplast proteostasis. Trends in Plant Sciences (TIPS) – prepublication online
Yuan, B., van Wijk, K.J. (2024) The chloroplast protease system degrades stromal DUF760-1 and DUF-2 domain-containing proteins at different rates. Plant Physiology
van Wijk, K.J., Leppert, T., Debley, E., Guzchenko, I., Sauermann, G., Routray, P., Sun, Q., Sun, Z., Mendoza, L., and Deutsch, E.W. (2024) The Zea mays PeptideAtlas – a new maize community resource. J Proteome Research 23(9):3984-4004.
van Wijk, K.J. (2024) Intra-chloroplast proteases; a holistic functional network view of chloroplast proteolysis. Plant Cell 36(9):3116-3130
Nancy A Eckardt, Tamar Avin-Wittenberg, Diane C Bassham , Poyu Chen, Qian Chen, Jun Fang, Pascal Genschik, Abi S Ghifari, Angelica M Guercio, Daniel J Gibbs, Maren Heese, R Paul Jarvis, Simon Michaeli, Monika W Murcha, Sergey Mursalimov , Sandra Noir, Malathy Palayam, Bruno Peixoto, Pedro L Rodriguez, Andreas Schaller, Arp Schnittger, Giovanna Serino, Nitzan Shabek, Annick Stintzi, Frederica L Theodoulou, Suayib Üstün, Klaas J van Wijk, Ning Wei, Qi Xie, Feifei Yu, Hongtao Zhang (2024) The lowdown on breakdown: Open questions in plant proteolysis (2024) The lowdown on breakdown: Open questions in plant proteolysis. Plant Cell 36(9):2931-2975.
van Wijk, K.J. and Adam, Z. (2024) Letter to the Editor: Does the polyubiquitination pathway operate inside intact chloroplasts to remove protein content? Plant Cell 36(9):2984-2989
van Wijk, K.J., Leppert, T., Sun, Q., Kearly, A., Nelson, A., Sun, Z., Debley, E., Guzchenko, I., Sauermann, G., Routray, P., Mendoza, L., and Deutsch, E.W. (2024). Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas. J. Proteome Research 23(1)185-214
van Wijk, K.J., Bentolilla, S., Leppert, T., Sun, Q., Sun, Z., and Deutsch, E.W. (2024) Accumulation and editing of the plastid- and mitochondrial-encoded proteome in Arabidopsis thaliana across plant parts and conditions through the PeptideAtlas. Plant Physiology 194(3) 1411-1430
van Wijk, K.J., Leppert, Zhi Sun, Eric W. Deutsch (2023). Does the ubiquitination degradation pathway really reach inside of the chloroplast? A re-evaluation of mass spectrometry-based assignments of ubiquitination. Journal of Proteome Research 22, 6, 2079–2091.
Rowland, E., Kim, J., Friso, G., Poliakov, A., Ponnala, L., Sun, Q., van Wijk, K.J. (2022). The CLP and PREP protease systems coordinate maturation and degradation of the chloroplast proteome in Arabidopsis thaliana. New Phytologist 236:1339–1357
Zhang, X., Hu, Y., Eme, L., Maruyama, S., Eveleigh, R.J.M, Curtis, B.A., Sibbald, S.J., Hopkins, J.F., Filloramo G.V., van Wijk, K.J., and Archibald, J.M. (2022) TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets. https://star-protocols.cell.com/protocols/1439
Liao, J-Y., R., Friso, G., Forsythe, Michel, E.J.S, Williams, A.M., Boguraev, S.S., Ponnala, L., Sloan, D.B., van Wijk, K.J. (2022) Proteomics, phylogenetics, and co-expression analyses indicate novel interactions in the plastid CLP chaperone-protease system. Journal of Biological Chemistry 298(3) 101609
Plant Cell consortium (2021) Vision, challenges and opportunities for a Plant Cell Atlas. Elife Sep 7;10:e66877. doi: 10.7554/eLife.66877.
Ishida, H., Okashita, Y., Ishida, H., Hayashi, M., Izumi, M., Makino, A., Bhuiyan, N.H., van Wijk, K.J. (2021) GFS9 affects piecemeal autophagy of plastids in young seedlings of Arabidopsis thaliana. Plant Cell Physiology 62(9) 1372-1386
van Wijk, K.J., Leppert, T., Sun, Q., Boguraev, S.S., Sun, Z., Mendoza, L., and Deutsch, E.W. (2021) The Arabidopsis thaliana PeptideAtlas; harnessing world-wide proteomics data for a comprehensive community proteomics resource. Plant Cell 33(11) 3421-3453
Bouchnak, I. and van Wijk, K.J. (2021) Structure, Function and Substrates of Clp AAA+ protease systems in cyanobacteria, plastids and apicoplasts; a comparative analysis. Journal Biological Chemistry Jan-Jun 2021;296:100338
(2020) Auto-catalytic processing and substrate specificity of Arabidopsis chloroplast glutamyl peptidase. Plant Physiology 184(1):110-129.
Watkins, K.P., Williams-Carrier, R., Chotewutmontri, P., Friso, G., Teubner, M., Belcher, S., Ruwe, H., Schmitz-Linneweber, C., van Wijk, K.J., Barkan. A. (2020) Exploring the proteome associated with the mRNA encoding the D1 reaction center protein of Photosystem II in plant chloroplasts. Plant Journal 102(2):369-382.
Bouchnak, I., and van Wijk, K.J. (2019) N-degron pathways in plastids. Trends in Plant Sciences 24(10):917-926.
Montandon, C., Friso, G., Liao, J.Y., Choi, J., van Wijk, K.J. (2019) In vivo trapping of candidate protease substrates and adaptors of the chloroplast CLPC1 chaperone. Journal of proteome Research 18(6):2585-2600.
Extreme variation in rates of evolution in the plastid Clp protease complex Plant Journal 98(2):243-259
Montandon, C., Dougan, D.A., van Wijk, K.J. (2019) N-degron Specificity of Chloroplast CLPS1 in Plants. FEBS letters 593(9):962-970
Liao, J-Y. R., van Wijk, K.J. (2019) Discovery of AAA+ protease substrates through trapping approaches. Trends in Biochemical Sciences 44(6):528-545.
Liao, J-Y.R., Friso, G., Kim, J., van Wijk, K.J. (2018) Consequences of the loss of catalytic triads in chloroplast CLPPR protease core complexes in vivo Plant Direct 2(10):e00086
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 29(11):2687-2710
Bhuiyan, N.H and van Wijk, K.J. (2017) Functions and substrates of plastoglobule-localized metallopeptidase PGM48. Plant Signalling and Behavior 12(6):e1331197.
van Wijk, K. J. and Kessler, F. (2017) Plastoglobuli: Plastid Microcompartments with Integrated Functions in Metabolism, Plastid Developmental Transitions, and Environmental Adaptation. Annual Review in Plant Biology 68, 253-289
Bhuiyan, N.H., Friso, G., Rowland, E., Majsec, K., van Wijk, K.J. (2016) Plastoglobule localized metallopeptidase PGM48 is a positive regulator of senescence in Arabidopsis thaliana. The Plant Cell 28(12):3020-3037
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
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
Lohscheider, J.N., Friso, G. and van Wijk, KJ. (2016) Phosphorylation of plastoglobular proteins in Arabidopsis thaliana. J. Exp Botany 67(13):3975-84
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
Friso, G. and van Wijk, K.J. (2015) Update: Post-translational protein modifications in Plant Metabolism. Plant Physiology 169, 1469-148
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):2677-91
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
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
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
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
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
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
van Wijk, K.J. (2015) Protein Maturation and Proteolysis in plant plastids, mitochondria and peroxisomes. Annual Review in Plant Biology 66:75-111.
Bhuiyan, N.H., Friso, G., Poliakov, A., Ponnala, L., 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.
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.
Nishimura, K and van Wijk, K.J. (2015) The Clp protease system in non-green plastids and chloroplasts. BBA 1847(9):915-30.
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)
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
Ponnala, L., Wang, Y., Sun, Q. and van Wijk, K.J. (2014) Correlation of mRNA and protein abundance in the developing maize leaf. Plant Journal 78(3):424-40
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
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. (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
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
Huang, M., Friso, G., Nishimura, K., Qu, X., Olinares, P.D.B., Majeran, W., Sun, Q., van Wijk, K.J. (2013) Construction of plastid reference proteomes for maize and Arabidopsis and evaluation of their orthologous relationships; the concept of orthoproteomics. Journal of Proteomics Research 4;12(1):491-504
Tian M., von Dahl C.C., Liu P.P., Friso G., van Wijk, K.J., Klessig D.F. (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
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.
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 159 (3), 961-974
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 17(9):546-55
Bentolila, S., Heller, W.P., Sun, T., Babina, A.M., Friso,G., van Wijk, K.J., and Hanson, M.R. (2012) Identification of a Protein Affecting Editing Efficiency at Most C Targets of Plant Organelle Editing. Proc Natl Acad Sci U.S.A. 109(22), E1453-146
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, 1172-1192
van Wijk, K.J. (2011) Plant Proteomics and Photosynthesis. Chapter 7, pp 151-173. In: Photosynthesis: Plastid Biology, 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
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
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
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 The Plant Cell 23(6):2348-6
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.
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
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.
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.
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.
Weise, S.E., van Wijk, K.J. and Sharkey, T.D. (2011) The role of transitory starch in C3, CAM, and C4 metabolism and opportunities for engineering leaf starch accumulation. J. Exp. Botany 62(9):3109-1
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
Hiren J Joshi, H.J., Matthias Hirsch-Hoffmann, M., Baerenfaller, K., Gruissem, W., Baginsky, S., Schmidt, R., Shulze, W.X., Sun,Q., van Wijk, K.J., Egelhofer, V., Wienkoop, S., Weckwerth, W., Bruley, W., Rolland, N., Toyoda, T., Nakagami, H., Jones, A.M.E., Briggs, S., Castleden, I., Tanz, S.K., Millar, A.H., Heazlewood, J.L. (2011) MASCP Gator: An aggregation portal for the visualizationof Arabidopsis proteomics data Plant Physiol. 155(1):259-70
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
Wickstrom, D., Wagner, S., Baars, L., Ytterberg, A.J., Klepsch, M., van Wijk, K.J., Luirink, J., de Gier, J.W. (2011) Consequences of depletion of the signal recognition particle in Escherichia coli. J Biol Chem. 286(6):4598-609.
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.
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
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
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
Kim, , 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
Zybailov, B., Friso, G., Kim, , 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
Kroeger, T.S., Watkins, K.P., Friso, G., van Wijk, K.J., and Barkan, A. (2009) A plant-specific RNA binding domain revealed through analysis of chloroplast group II intron splicing. PNAS 106(11):4537-42
Majeran, W., and van Wijk, K.J. (2009) Cell-type specific differentiation of chloroplasts in C4 plants. Trends in Plant Science 14(2):100-
Sun, Q., Zybailov, B., Majeran, W., Friso, G., Olinares, P.D.B., van Wijk, K.J. (2009) PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res. (database issue) 37: D969
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
Prikryl, J., Watkins, K.P., Friso, G., van Wijk, K.J,. 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. 16:5152-65.
Klepsch, M., Schlegel, S., Wickström, D., Friso, G., van Wijk, K.J., Persson, J.O., de Gier, J.W., Wagner, S. (2008) Immobilization of the first dimension in 2D blue native/SDS-PAGE allows the relative quantification of membrane proteomes. 2008 Jul 29.
Rutschow, H., Ytterberg, A.J., Friso, G., Nilsson, R., van Wijk, K.J. (2008) Quantitative proteomics of a chloroplast SRP54 sorting mutant and its genetic interactions with CLPC1 in Arabidopsis thaliana. Plant Physiol. 148(1):156-75.
Majeran, W., Zybailov, B., Ytterberg, A.J., Dunsmore, J., Sun, Q., van Wijk, K.J. (2008) Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells. Mol Cell Proteomics. 9:1609-3
Zybailov, B., Rutschow, H., Friso, G., Rudella, A., Emanuelsson, O., Sun, Q., van Wijk, K.J. (2008) Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS ONE. Apr 23;3(4)
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
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.
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
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.
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
Brehelin, C., Kessler, F., van Wijk, K.J. (2007) Plastoglobules: versatile lipoprotein particles in plastids. Trends in Plant Science 12(6):260-266
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.
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
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), 1704-172
Giacomelli, L., 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
van Wijk, K.J. Peltier, J.B., Giacomelli, L. (2007) Isolation of chloroplast proteins from Arabidopsis thaliana for proteome analysis. Methods Molecular Biology 355:43-8.
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
van Wijk, K.J. (2006) Expression, Prediction and Function of the thylakoid proteome in higher plants and green algae, pp. 125-143. 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.
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
Zabrouskov, , 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.
Baars, L. Ytterberg, A.Y., Drew, D., Wagner, S., Thilo, C., van Wijk, K.J. and de Gier, J.W. (2006) Defining the role of the E. coli chaperone SECB using comparative proteomics. Biol. Chem 218, 10024-10034
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 Proteomic 5.1, 114-133
Majeran, W., Cai, Y., Sun, Q., van Wijk, K.J. (2005) Functional differentiation of Bundle Sheath and Mesophyll maize chloroplasts determined by Comparative proteomics. The Plant Cell 17(11) 3111-40
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
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
van Wijk,K.J. (2004) Chloroplast Proteomics. Chapter 14, pp 329-358. In Plant Functional Genomics, D Leister, Editor. The Haworth Press, Inc. Binghamton, NY.
van Wijk, KJ. (2004) Plastid Proteomics. Plant Physiology and Biochemistry 42, 963-97
Labate, M.T. V., Ko, K., Ko, Z.W., Costa Pinto, L.S.R., Real, M.J.U.D., Romano, M.,Barja, P.R., ranell, 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
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
Suzuki, J. Y., Ytterberg, A.Y., Beardslee, T., Allison, L.A., van Wijk, K.J., and Maliga, P. (2004) Composition of the affinity purified plastid RNA polymerase core and in vitro reconstitution of the holoenzyme. Plant Journal 40(1), 164-172
Sun, Q., Olof Emanuelsson, O., van Wijk, K.J. (2004) Analysis of curated and predicted plastid subproteomes of Arabidopsis thaliana; Subcellular compartmentalization leads to distinctive proteome properties. Plant Physiology 135, 723-734
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
Peltier*, J.B, Ripoll*, D, Friso, G. Rudella, A.,, Ytterberg, J., Cai, Y., Giacomelli, L., Pillardy, J and van Wijk, K.J. (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
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. and Cell. Proteomics 2.12, 1253-1260
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
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
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
Peltier J-B., Emanuelsson, Kaluma, D.E., Ytterberg, Y. Friso, G., Rudella, A., Roepstorff, von Heijne, G. and van Wijk, KJ. (2002) Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis thaliana determined by experimentation and genome-wide prediction Plant Cell 14, 211-236
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
Fröderberg, L., Röhl, T., van Wijk, K.J., de Gier, J.W. (2001) Chloroplast SecE can functionally complement the coli homologue. FEBS Letters 24919, 1-5
van Wijk, K.J. (2001) Update on plant proteomics. Challenges and Prospects of Plant Proteomics Plant Physiology 126, 501-50
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
van Wijk, K.J. (2000) Proteomics of the chloroplast; Experimentation and prediction. Trends in Plant Science 5, 420-425
Zhang, L., Paakkarinen,V., van Wijk, K.J., 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
Peltier, J.-B., Friso, G., Kalume, D.E., Roepstorff, P, Nilsson, F., Adamska, I., van Wijk, K.J. (2000) Proteomics of the chloroplast: Systematic identification and targeting analysis of thylakoid proteins. Plant Cell 12, 319-341
Zhang, L., Paakkarinen,V., van Wijk, K.J., Aro, E-M (1999). Co-translational assembly of the D1 protein into Photosystem II complexes. J. Biol. Chem. 274, 16062-16067
Houben, E., J.W. de Gier 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
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
1994-1998. From my postdoctoral period
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
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
van Wijk, K.J., M. Roobol-Boza, R. Kettunen, B. Andersson 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, 6178-6168van Wijk, K.J. and L. Eichacker (1996) Light triggers release of polysome bound D1 protein and integration into Photosystem II. FEBS Lett. 388, 89-93
van Wijk, K.J., B. Andersson and E-M. Aro (1996) Kinetic resolution of the incorporation of the D1 protein into PSII and localisation of assembly intermediates in thylakoid membranes of spinach chloroplasts. J. Biol. Chem. 271, 9627-9636
van Wijk, K.J., S. Bingsmark, E.M. Aro and B. Andersson (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. Chem. 270, 25685-25696
van Wijk, K.J., Knott, T. and C. Robinson (1995) Evidence for Sec A and dpH independent insertion of D1 into thylakoids. FEBS lettt. 368, 263-266
van Wijk, K.J., Nilsson, L.O., Styring, S. (1994) Synthesis of reaction centre proteins and reactivation of redox components during repair of photosystem II after light-induced inactivation. J. Biol. Chem 269, 28382-28392
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. Chem. 269, 5115-5121
1990-1993. From my MS and PhD thesis
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
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
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
van Wijk, K.J., B. Andersson and S. Styring. (1992) Spectroscopic characterization of photoinhibited photosystem II and kinetic resolution of the triggering of the D1-reaction center protein for degradation. Biochim. Biophys. Acta (Biomembranes) 1100, 207-215
van Wijk, K.J. and G.H. Krause. (1991) O2dependence of photoinhibition at low temperatures in intact protoplast of Valerianella locusta L. Planta 186, 135-142
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
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