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We are studying several aspects of chloroplast biology in plants. Chloroplasts contain ~3000 different proteins that together carry out important functions. In addition to producing molecular oxygen and carbohydrates through photosynthesis, making life on earth possible, chloroplasts make many other important products, including vitamins A, E and K1.

Our research is currently divided in three main themes:

i) organellar protein homeostasis (proteostasis) through coordinated action of proteolytic systems in chloroplastsChloroplasts contains several thousand different proteins, some with a high number of copies (e.g. Rubisco) and other with very low copy number. Some proteins have a very short half-life of just ~30 min, whereas others are stable for several days. Chloroplasts contain many different protease systems encoded by ~100 genes. Research in the van Wijk lab aims to determine what controls the stability of chloroplast proteins.  We are particularly interested to determine the signals/information within proteins that are recognized by different proteases; such signals are called degrons and hold the key to understanding proteolysis.  We are study the coordination of protease activity with the metabolic state of chloroplasts, and integration of different protease activities (i.e. protease networks). We mainly use Arabidopsis, but also maize, as our experimental system and we generated many single and higher order chloroplast protease mutants to study genetic and functional interactions within the protease network. A variety of proteomics and mass spectrometry techniques (e.g. TAILS) are used to track, identify and quantify N-terminal maturation, proteolytic cleavage events and accumulation of protein degradation products. In planta substrate trapping and affinity enrichment further help to identify substrates and discover protein-protein interactions, e.g. resulting recently in our discovery of a new adaptor ClpF. This research is funded by the National Science Foundation (NSF).

ii) chloroplast lipid micro-compartments, named plastoglobules (PG). Chloroplasts in leaves but also chromoplasts in fruits and flowers, and other plastid types in non-photosynthetic tissues, contain dynamic lipid-protein monolayer particles (PG).  These particles are filled with vitamin E (tocopherol), and various other isoprenoids such as plastochromanol-8 and plastoquinone, as well as vitamin K1. These PGs function in the metabolism of these isoprenoids but are also important for recycling of the lipids and pigments (e.g. chlorophyll and carotenoids) in thylakoid membranes during abiotic stresses and during senescence. Using mass spectrometry, we identified more than 30 proteins in these PG; some have known functions such as tocopherol cyclase (VTE1) involved in vitamin E biosynthesis, whereas the functions of most others are unknown. The van Wijk lab studies how PG and its proteins contribute to plant metabolism, leaf development and aging as well as abiotic stress defense. For instance, we observed that null mutants for several PG localized ABC1 kinases are light sensitive and also cannot cope well with nitrogen starvation. Understanding the function of these PG is essential for understanding chloroplast metabolism and stress responses, ultimately providing opportunities for more stress resistant plants and increased agricultural production. For an overview of PG functions,  read van Wijk and Kessler (2017).

iv) Plant proteomics and PPDB.  Proteins carry out cellular metabolic, regulatory and structural functions. Therefore understanding the protein composition of cells and subcellular compartments, the proteome, is essential to understand biology. Proteomes can be identified and quantified using modern mass spectrometry, when combined with genome sequencing and bioinformatics. The van Wijk lab is using mass spectrometry as a key tool to characterize plant and chloroplast proteomes, protein-protein interactions, and protein up-and down regulation, as well as proteolysis. To that end we use a variety of biochemical techniques such as cross-linking and N-terminal labeling with stable isotopes. We established the Plant Proteome Database (PPDB) in 2006 which serves to display proteome information for Arabidopsis, maize and rice (Sun et al., 2009). As part of the PPDB, we identify and annotate plastid/chloroplast proteins based on experimentation, bioinformatics including co-expression networks, and curation of literature (see e.g. Huang et al 2013)

Most of our research is currently supported by the National Science Foundation (NSF).

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