Research in the van Wijk lab is divided in two main themes:
- Control of organellar protein homeostasis (termed proteostasis) through coordinated action of proteolytic systems in mitochondria and chloroplasts. Key questions are the identification of degrons (i.e. the recognition signals/information within mitochondrial and chloroplast proteins that are recognized by different proteases) in particular N-degrons, coordination/integration of protease activity with the metabolic state of the organelles and cells, and integration of protease activities (i.e. protease networks).
- The role of lipid micro-compartments, named plastoglobules (PG), within chloroplasts to coordinate organelle metabolism. The key question is how PG coordinate different metabolic processes and pathways. For instance, we observed that null mutants for several PG localized ABC1kinases lack accumulation of starch and have modified isoprenoid metabolite profiles and conditional phenotypes.
We are solving these biological questions through an interdisciplinary approach including molecular genetics, protein biochemistry, X-ray crystallography (through collaboration), mass-spectrometry-driven proteomics and metabolomics, as well as in silico systems analysis (e.g. mRNA-based co-expression networks). To support the proteomics workflow, the van Wijk lab has in-house mass spectrometers, an in-house Plant Proteome Data Base (PPDB) seamlessly connected to our in-house MS-data analysis pipeline; graduate students and postdocs are trained in MS and collectively maintain our instrumentation.
Outreach and Extension Focus
Outreach is focused on multi-disciplinary training in quantitative plant biology and biochemistry, as well as bioinformatics and statistics at the undergraduate, graduate and post-doctoral levels. Through the successful summer internship NSF sponsored plant genome, we involve undergraduates from under-represented groups in our research.
Teaching Focus
Van Wijk`s class room teaching is focused on Plant Biochemistry (BioPL462), Plant Genomics Tools and Techniques (BioPL641) and Plant Proteomics and Mass Spectrometry (BioPL482/483 series). In addition, van Wijk frequently participates in Workshops on Plant Genomics, where he typically teaches proteomics and mass spectrometry. Research advising occurs at the undergraduate, graduate and post-doctoral levels and is oriented towards training in multi-disciplinary research with the objective to understand plastid differentiation and protein homeostatis/proteolysis.
Journal Publications
Google Scholar profile and publications.
- van Wijk, K., & Kessler, F. (2017). Plastoglobuli: Plastid Microcompartments with Integrated Functions in Metabolism, Plastid Developmental Transitions, and Environmental Adaptation. Annual Review of Plant Biology. 68:253-289.
- Bhuiyan, N. H., Friso, G., Rowland, E., Majsec, K., & van Wijk, K. (2016). The Plastoglobule-Localized Metallopeptidase PGM48 is a Positive Regulator of Senescence in Arabidopsis thaliana. The Plant Cell. 28:3020-3037.
- van Wijk, K. (2015). Protein Maturation and Proteolysis in plant plastids, mitochondria and peroxisomes. Annual Review of Plant Biology. 66:75-111.
- Ponnala, L., Wang, Y., Sun, Q., & van Wijk, K. (2014). Correlation of mRNA and protein abundance in the developing maize leaf. The Plant Journal. 78:424-40.
- Nishimura, K., & van Wijk, K. (2014). The Clp protease system in non-green plastids and chloroplasts. Biochimica et Biophysica Acta (BBA): Bioenergetics.
- van Wijk, K., Friso, G., Walther , D., & Schulze, W. X. (2014). Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs. The Plant Cell. 26:2367Ð2389.
- Nishimura, K., Asakura, Y., Friso, G., Kim, J., Oh, H., Rutschow, H., Ponnala, L., & van Wijk, K. (2013). ClpS1 is a conserved substrate selector for the chloroplast Clp protease system in Arabidopsis thaliana. The Plant Cell. 25:2276-2301.
- Olinares, P., Kim, J., Davis, J. I., & van Wijk, K. (2011). Subunit stoichiometry, evolution, and functional implications of an asymmetric plant plastid ClpP/R protease complex in Arabidopsis. The Plant Cell. 23:2348-2361.
- Otinares, P. D., Ponnala, L., & van Wijk, K. (2010). Megadalton Complexes in the Chloroplast Stroma of Arabidopsis thaliana characterized by Size Exclusion Chromatography. MCP: Molecular & Cellular Proteomics. 9:1594-1615.
- Friso, G., Majeran, W., Huang, M., Sun, Q., & van Wijk, K. (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.
Presentations and Activities
- Chloroplast protein maturation and degradation in Arabidopsis thaliana. Conference on N-end rule pathways. September 2017. Proteostasis network . Halle, Germany.
- Methods and contributions of proteomics and mass spectrometry to understanding plant chloroplast biology. 7th Symposium of the Mexican Proteomics Society | Mass Spectrometry Based Omic . September 2017. HUPO. Guadalajara.
- The plastid protein life-cycle and the plastid peptidase network in Arabidopsis. Gordon Conference on Chloroplast Biotechnology . January 2017. GRC. Ventura, CA.
- Protein maturation & proteolysis in chloroplasts. American Society of Plant Biologists: ASPB 2016. July 2016. Austin, TX.
- Chloroplast protein maturation and N-terminal stability. Gordon Conference on Chloroplast Biotechnology. January 2015. GRC. Ventura, CA.
