Networks
Van Wijk, Klaas
Cornell Faculty Member
Positions
After completing his B.Sc. and M.Sc. at the Agricultural University Wageningen (Netherlands), van Wijk obtained a PhD at the University of Groningen (The Netherlands). This was then followed by postdocs at the Dept. of Biochemistry, Stockholm University, Sweden and at the Carnegie Institute at Stanford University (CA). He then became assistant professor in 1997 at the Dept. of Biochemistry, Stockholm University and moved his lab in 2001 to Cornell University. In 2005 he was promoted to tenured associate professor level. In 2007 he became DGS for the Field of Plant Biology
Research Areas
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- Service
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Affiliations
advisory group member
Research
research overview
- Plastids are essential organelles of prokaryotic origin present in nearly every plant cell containing an estimated 3000-4000 different proteins. Chloroplasts are the best known green plastids and carry out photosynthesis and also synthesize various primary and secondary metabolites. The van Wijk lab is focused on i) bundle sheath and mesophyll cell specific differentiation of chloroplasts in leaves of the C4 plant maize, and ii) in chloroplast biogenesis and protein homeostasis in Arabidopsis thaliana, with a particular focus on the Clp protease machinery. We use a multi-disciplinary approach, with emphasis on large scale comparative proteomics and mass spectrometry, bioinformatics and reverse genetics. Protein identifications with associated information are uploaded into the Plant Proteome Data Base (http://ppdb.tc.cornell.edu/), building a foundation for systems biology of the Arabidopsis and maize proteomes. Our proteomics and mass spectrometry infrastructure and expertise are also used in collaborations with colleagues at Cornell University and elsewhere.
principal investigator on
- GEPR: A SYSTEMS APPROACH TO THE DEVELOPMENT AND FUNCTION OF C4 PHOTOSYNTHESIS awarded by DIRECTORATE FOR BIOLOGICAL SCIENCES NSF 2012 - 2016
- GEPR: MACROMOLECULAR NETWORKS UNDERLYING CHLOROPLAST BIOGENESIS awarded by NATL SCIENCE FOUNDATION 2009 - 2013
- SELECTION AND DELIVERY OF SUBSTRATES TO THE ESSENTIAL CLP PROTEASE COMPLEX IN PLASTIDS OF ARABIDOPSIS THALIANA awarded by DIRECTORATE FOR BIOLOGICAL SCIENCES NSF 2010 - 2013
- THE ARABIDOPSIS SALICYLIC ACID SIGNALING NETWORK: A PARADIGM FOR PHYTOHORMONE SIGNALING awarded by NATL SCIENCE FOUNDATION 2009 - 2013
co-principal investigator on
keywords
- Arabidopsis thaliana
- maize
- mass spectrometry
- plant biochemistry
- plastid biogenesis
- protein sorting
- proteolysis
- proteomics
submitted impact statement
- The central role of plastids in plant development, their role in growth, metabolism and stress reponse, and the construction of a public plastid database
- The central role of plastids in plant development, growth and metabolism and stress reponse and a public plastid database
- Leaf development and cell specific differentiation in maize and rices and chloroplast protein homeostasis and proteolysis in Arabidopsis
- Differentiation, protein homeostasis and proteolysis of essential chloroplasts in Arabidopsis and maize
Publications
individual publications
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academic article
- 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. 159:961-974. 2012
- Construction of plastid reference proteomes for maize and Arabidopsis and evaluation of their orthologous relationships; the concept of orthoproteomics.. Journal of Proteomics Research. 2012
- ABC1K atypical kinases in photosynthetic organisms; filling the organellar kinase void.. Trends in Plant Science. 17:546-555. 2012
- Nucleoid-enriched proteomes in developing plastids and chloroplasts from maize leaves; a new conceptual framework for nucleoid functions.. Plant Physiology. 158:156-189. 2012
- RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Proceedings of the National Academy of Sciences of the United States of America. 109. 2012
- The Purification of the Chlamydomonas reinhardtii chloroplast ClpP complex: additional subunits, domains and structural features. Plant Molecular Biology. 80:189-202. 2012
- The combined use of photoaffinity labeling and surface plasmonresonance-based technology identifies multiple salicylic acid-binding proteins.. The Plant Journal. 72:1027-1038. 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. 2012
- A plasmodesmata-localized protein mediates a crosstalk between cell-to-cell communication and innate immunity in Arabidopsis.. The Plant Cell. 23:3353-3357. 2011
- APO1 promotes the splicing of chloroplast group II introns and harbors a novel plant-specific RNA binding domain. The Plant Cell. 23:1082-92. 2011
- Characterization of the Consequences of YidC Depletion on the Inner Membrane Proteome of E. coli Using 2D Blue Native/SDS-PAGE.. Journal of Molecular Biology. 409:124-135. 2011
- Large-Scale Label-Free Quantitative Proteomics of the Pea aphid-Buchnera Symbiosis.. Molecular Cell Proteomics. 10. 2011
- MASCP Gator: An aggregation portal for the visualization of Arabidopsis proteomics data.. Plant Physiology. 155:259-70. 2011
- Plastid Proteomics in Higher Plants: Current State and Future Goals. Plant Physiology. 155:1578-88. 2011
- Subunit stoichiometry, evolution, and functional implications of an asymmetric plant plastid ClpP/R protease complex in Arabidopsis. . The Plant Cell. 23:2348-2361. 2011
- The Clp protease system; a central component of the chloroplast protease network.. Biochimica et Biophysica Acta. 1807:999-1011. 2011
- The role of transitory starch in C3, CAM, and C4 metabolism and opportunities for engineering leaf starch accumulation.. Journal of Experimental Botany. 62:3109-18. 2011
- The workflow for quantitative proteome analysis of chloroplast development and differentiation, chloroplast mutants and protein interactions by spectral counting. Methods Molecular Biology. 775:265-282. 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. 11:1559-1568. 2011
- Consequences of depletion of the signal recognition particle in Escherichia coli. Journal of Biological Chemistry. 2010
- Megadalton Complexes in the Chloroplast Stroma of Arabidopsis thaliana characterized by Size Exclusion Chromatography. Molecular & Cellular Proteomics. 9:1594-1615. 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. 2010
- Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize. The Plant Cell. 22:3509-3542. 2010
- 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. 81:8015-24. 2009
- A plant-specific RNA binding domain revealed through analysis of chloroplast group II intron splicing. Proceedings of the National Academy of Sciences of the United States of America. 106:4537-42. 2009
- Cell-type specific differentiation of chloroplasts in C4 plants. Trends in Plant Science. 14:100-9. 2009
- PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Research. 37. 2009
- A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis. Nucleic Acids Research. 16:5152-65. 2008
- Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells. Mol Cell Proteomics. 9:1609-38. 2008
- Effects of SecE depletion on the inner and outer membrane proteomes of Escherichia coli. Journal of Bacteriology. 190:3505-25. 2008
- Immobilization of the first dimension in 2D blue native/SDS-PAGE allows the relative quantification of membrane proteomes. Methods. 46:48-53. 2008
- Quantitative proteomics of a chloroplast SRP54 sorting mutant and its genetic interactions with CLPC1 in Arabidopsis thaliana. Plant Physiology. 148:156-75. 2008
- Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLOS One. 3. 2008
- Tuning Escherichia coli for membrane protein overexpression. Proceedings at the National Academy of Science USA. 105:14371-6. 2008
- A Ribonuclease III Domain Protein Functions in Group II Intron Splicing in Maize Chloroplasts. The Plant Cell. 19:2606-2623. 2007
- A comprehensive analysis of the 14-3-3 interactome in barley leaves using a complementary proteomics and two-hybrid approach. Plant Physiology. 143:670-83. 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. 2007
- Arabidopsis thaliana deficient in two chloroplast ascorbate peroxidases shows accelerated light-induced necrosis when levels of cellular ascorbate are low. Plant Molecular Biology. 65:627-644. 2007
- Consequences of membrane overexpression in Escheria coli. Molecular Cellular Proteomics. 6:1527-1550. 2007
- Isolation of chloroplast proteins from Arabidopsis thaliana for proteome analysis. Methods Molecular Biology. 335:43-48. 2007
- Plastoglobules: versatile lipoprotein particles in plastids. Trends in Plant Science. 12:260-266. 2007
- Defining the role of the E. coli chaperone SECB using comparative proteomics. Journal of Biological Chemistry. 218:10024-10034. 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. 18:1704-1721. 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. 141:685-701. 2006
- Protein profiling of plastoglobules in chloroplasts and chromoplasts; a surprising site for differential accumulation of metabolic enzymes. Plant Physiology. 140:984-997. 2006
- Recent advances in the study of Clp, FtsH and other proteases located in chloroplasts. Current Opinion in Plant Biology. 9:234-240. 2006
- Stepwise Deamidation of Ribonuclease A at Five Sites Determined by Top Down Mass Spectrometry. Biogeochemistry. 45:987-992. 2006
- The oligomeric stromal proteome of A. thaliana chloroplasts. Mol Cell Proteomic. 5:114-133. 2006
- A scalable, GFP-based pipeline for membrane protein overexpression screening and purification. Protein Science. 14:2011-2017. 2005
- Functional differentiation of Bundle Sheath and Mesophyll maize chloroplasts determined by Comparative proteomics. The Plant Cell. 17:3111-3140. 2005
- The chloroplast ClpP complex in Chlamydomonas reinhardtii contains an unusual high molecular mass subunit with a large apical domain. FEBS Journal. 272:5558-5571. 2005
- Analysis of curated and predicted plastid subproteomes of Arabidopsis thaliana; Subcellular compartmentalization leads to distinctive proteome properties. Plant Physiology. 135:723-734. 2004
- Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted 3-D structures and functional implications. Journal of Biological Chemistry. 279:4768-4781. 2004
- Composition of the affinity purified plastid RNA polymerase core and in vitro reconstitution of the holoenzyme. Plant Journal. 40:164-172. 2004
- Constitutive expression of pea LHCb1.2 in tobacco affects plant development, morphology and photosynthetic capacity. Plant Molecular Biology. 55:701-714. 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. 2004
- New functions of the thylakoid membrane proteome of Arabidopsis thaliana revealed by a simple, fast and versatile fractionation strategy. Journal of Biological Chemistry. 279:49367-49383. 2004
- Plastid Proteomics. Plant Physiology and Biochemistry. 42:963-977. 2004
- A new mass spectrometry approach for Plant proteomics: characterization of chloroplast proteins of Arabidopsis thaliana by top down mass spectrometry. Molec. and Cell. Proteomics 2. 12:1253-1260. 2003
- Expression of tetanus toxin fragment C in tobacco chloroplasts. Nucleic Acids Research. 31:1174-1179. 2003
- Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis thaliana determined by experimentation and genome-wide prediction. Plant Cell. 14:211-236. 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. 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. 2002
- Complementation of bacterial SecE by a chloroplastic homologue. FEBS Letters. 498:52-56. 2001
- Identification of a 350 kDa chloroplast ClpP protease complex by BN-PAGE and Mass spectrometry. J. Biol. Chemistry. 276:16318-16327. 2001
- In vitro Reconstitution of Insertion and Processing of Cytochrome f in a Homologous Chloroplast Translation System J. Biol. Chemistry. FEBS Letters. 276:35465-35472. 2001
- Update on plant proteomics. Challenges and Prospects of Plant Proteomics. Plant Physiology. 126:501-508. 2001
- Biogenesis of the chloroplast-encoded D1 protein: Regulation of mechanisms of D1 protein translation elongation, insertion and assembly. Plant Cell. 12:1769-1781. 2000
- Proteomics of the chloroplast: Systematic identification and targeting analysis of thylakoid proteins. Plant Cell. 12:319-341. 2000
- Proteomics of the chloroplast; Experimentation and prediction. Trends in Plant Science. 5:420-425. 2000
- Co-translational assembly of the D1 protein into Photosystem II complexes. J. Biol. Chem. 274:16062-16067. 1999
- Insertion of leader peptidase into the thylakoid membrane during synthesis in a chloroplast translation system. Plant Cell. 11:1553-1564. 1999
- Interactions of ribosome nascent chain complexes of the chloroplast-encoded D1 thylakoid membrane protein with cpSRP54. EMBO Journal. 18:733-742. 1999
- Expression of a dominant negative form of SRP54 inhibits chloroplast biogenesis in Arabidopsis thaliana. Plant Journal. 13:177-186. 1998
- PsbA gene expression in pea leaves during high light stress and subsequent recovery. Eur. J Biochemistry. 247:441-448. 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. 1997
- Kinetic resolution of the incorporation of the D1 protein into PSII and localisation of assembly intermediates in thylakoid membranes of spinach chloroplasts. Journal of Biological Chemistry. 271:9627-9636. 1996
- Evidence for Sec A and dpH independent insertion of D1 into thylakoids. FEBS Letters. 368:263-266. 1995
- In vitro synthesis and incorporation of PSII core proteins: the D1 protein can be incorporated into Photosystem II in isolated chloroplasts and thylakoids. Journal of Biological Chemistry. 270:25685-25696. 1995
- 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. Journal of Biological Chemistry. 269:5115-5121. 1994
- Synthesis of reaction centre proteins and reactivation of redox components during repair of photosystem II after light-induced inactivation. Journal of Biological Chemistry. 269:28382-28392. 1994
- Kinetic resolution of different recovery phases of photoinhibited Photosystem II in cold-acclimated and non-acclimated spinach leaves. Physiol. Plantarum. 87:187-183. 1993
- Photoinhibition and recovery of Photosystem II in relation to heterogeneity. Biochim. Biophys. Acta (Biomembranes). 1142:59-68. 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. 1993
- 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. 1992
- O2dependence of photoinhibition at low temperatures in intact protoplast of Valerianella locusta L. Planta. 186:135-142. 1991
- Physiological effects of long term exposure to low concentrations of SO2 and NH3 on poplar leaves. Physiol. Plantarum. 82:32-40. 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. 1990
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chapter
- Plant Proteomics and Photosynthesis. . Photosynthesis: Plastid Biology, Energy Conversion and Carbon Assimilation. 151-173. 2011
- Isolation of chloroplast proteins from Arabidopsis thaliana for proteome analysis. Plant Proteomics: Methods and Protocols (Methods in Molecular Biology ). 43-48. 2007
- Expression, Prediction and Function of the thylakoid proteome in higher plants and green algae. The Structure and Function of Plastids. 125-143. 2006
- Expression, Prediction and Function of the thylakoid proteome in higher plants and green algae. The Structure and Function of Plastids. 2005
- Chloroplast Proteomics. Plant Functional Genomics. 329-358. 2004
- Chloroplast Proteomics. Plant Functional Genomics. 329-358. 2004
- Proteins involved in Biogenesis of the thylakoid membrane, In Regulation of Photosynthesis. Kluwer Academic Publishers. 153-175. 2001
- Photosynthesis. In: Encyclopedia of Molecular Biology. John Wiley and Sons, Inc. 1999
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conference paper
- Weaponry revealed: secreted proteins of Erwinia amylovora. Phytopathology. 2002
featured in archived article
speaker at Cornell event
Teaching
teaching activities
- BIOPL-7490: Graduate Research in Botany - Spring 2013
- BIOPL-7490: Graduate Research in Botany - Fall 2012
- BIOPL-4620: Plant Biochemistry - Spring 2012
- BIOPL-7490: Graduate Research in Botany - Spring 2012
- BIOMG-6410: Laboratory in Plant Molecular Biology - Fall 2011
- BIOPL-4832: Plant Molecular Biology I: Proteomics in Plant Biology - Fall 2011
- BIOPL-6410: Laboratory in Plant Molecular Biology - Fall 2011
- BIOPL-7430: Faculty Research in Plant Cell and Molecular Biology - Fall 2011
- BIOPL-7490: Graduate Research in Botany - Fall 2011
- PLBR-4832: Plant Molecular Biology I: Proteomics in Plant Biology - Fall 2011
- PLPA-4832: Plant Molecular Biology I: Proteomics in Plant Biology - Fall 2011
Service
service to the profession
- Scientific Opportunities Team - iPlant collaborative Member 2009 -
- Multinational Arabidopsis Steering Subcommittee on Proteomics Chairperson 2008 -
- American Society of Mass Spectrometry
- Session 'Plant Proteomics' - World Congress in Botany Chairperson - 2005
- Advisory workshop on ‘Systems Biology’, Dept. of Energy, CA Member - 2003
reviewer or editor for
event host
Background
education and training
- Ph.D. in, University of Groningen 1992
- M.S. in, University of Wageningen 1988
- University of Wageningen 1982
awards and honors
Other
college
- CALS
research keyword
- Arabidopsis thaliana
- maize
- mass spectrometry
- plant biochemistry
- plastid biogenesis
- protein sorting
- proteolysis
- proteomics