Welcome to the van Wijk lab

We are studying chloroplast biology in plants; key words for our chloroplast research are proteostasis, degrons, protease networks, biogenesis and differentiation. 

Chloroplasts contain ~3000 different proteins that together carry out  important functions. In addition to producing molecular oxygen that makes life on earth possible, chloroplasts synthesize a number of important products, including vitamins A, E and K1 and various anti-oxidants. We study unique aspects of chloroplast biology in Arabidopsis thaliana (thale cress) and maize. In particular, we aim to determine the life-cycle of chloroplast proteins: how do they mature,  which proteases (such as CLP) degrade them, and how are these proteins recognized (degrons) by these proteases (van Wijk 2015). In other words, what governs chloroplast proteostasis.  Finally we explore how the function and structure of chloroplasts, and other plastid types, are linked to cell-type; examples are differentiating chloroplasts in bundle sheath and mesophyll cells in C4 plants, such as maize (for more details).

Harnessing world-wide proteomics mass spectrometry data sets from Arabidopsis and maize to create species specific PeptideAtlasses. A major limitation of plant research is the accurate identification and quantification of proteins from tissues and organisms. Mass spectrometry is a technology that allows scientists to identify thousands of proteins from a tissue or organism. Together, the collective set of all proteins is called the “proteome”. Through an NSF sponsored project we are generating an atlas of identified proteins in the model plant species Arabidopsis thaliana using publicly available protein mass spectrometry studies from laboratories around the world. Such an atlas allows the researchers to address a number of important biological questions about this plant proteome. We are also generating an atlas for maize B73 and W22 which will be released in the Summer of 2023. This project will also educate and train young scientists in techniques for processing and managing mass spectrometry data for understanding the proteome of plants. In 2021 we released the first Arabidopsis PeptideAtlas  http://www.peptideatlas.org/builds/arabidopsis/  as described in the publication van Wijk et al (2021) The Plant Cell. In 2023 we will release the second build of this atlas based on even more mass spec data. This is a collaboration with the Institute for Systems Biology (ISB) in Seattle.

Methodologies. We employ an interdisciplinary approach including  molecular genetics especially using Arabidopsis (we have generated a large collection of protease mutants and tagged protease lines), protein biochemistry, mass spectrometry, proteomics and metabolomics, as well as in silico (bioinformatics) systems analysis (e.g. mRNA-based co-expression networks),  and through collaborations also Cryo-EM and X-ray crystallography.  The van Wijk lab has an in-house mass spectrometer (Q-Exactive), an extensive bioinformatics proteomics processing ‘pipe-line’ and houses the Plant Proteome Data Base (PPDB).

Brief biography van Wijk

Follow us:  @vanwijklab or ResearchGate or Google Scholar