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 two main themes:
i) chloroplast protein homeostasis (proteostasis) through coordinated action of proteolytic systems in chloroplasts. Chloroplasts 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) Plant proteomics, PPDB and the PeptideAtlas. 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. We are using mass spectrometry as a key tool to characterize plant and chloroplast proteomes, protein-protein interactions, and proteolysis. 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. We recently established the first build of the Arabidopsis PeptideAtlas based on publicly available protein mass spectrometry studies from laboratories around the world collected through ProteomeXchange. see the preprint at BioRxiv. This is a collaboration with the Institute for Systems Biology (ISB) in Seattle.
Most of our research is currently supported by the National Science Foundation (NSF).