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Krijgsveld Team

Functional proteomics

The Krijgsveld team uses biochemical and mass spectrometric approaches to understand the dynamics of protein expression and interaction in the context of cellular differentiation and stress response.

Krijgsveld Team

Changes in protein expression during reprogramming of fibroblasts (A, B) leading to the formation of induced pluripotent stem cells (C).

Previous and current research

Proteins fulfill most of the functions that are crucial in establishing cellular phenotypes. In addition, it is becoming increasingly clear that proteins rarely act alone, but that they constitute intricate networks, both among themselves and with other biomolecules. This system is both robust and dynamic, allowing a cell to respond to external cues, or to develop from an embryonic to a mature state. Our interest is in understanding cellular properties from this perspective, realising that one needs to study proteins collectively rather than in isolation, and dynamically rather than under static conditions.

Our research is centred on quantitative proteomics, combining biochemistry, mass spectrometry, analytical chemistry, and bioinformatics, applied to various biological systems (yeast, Drosophila, mammalian cells). Our main interest is to understand how changes in protein expression, localisation and interaction underlie processes in stress-response, differentiation and reprogramming. For instance, large-scale proteomic experiments enable us to characterise the proteomes of highly purified mouse hematopoietic stem cells and progenitor populations obtained by fluorescence-activated cell sorting, generating novel insights in the initial steps of hematopoiesis in vivo. Furthermore, we have performed time course analyses quantifying the proteome changes in fibroblasts during their reprogramming to induced pluripotent stem cells (iPSCs), identifying and functionally validating proteins that are key in the gain of pluripotency. Apart from these large-scale analyses of intracellular proteomes, we have developed new tools to study secretory proteins and their role in cell signalling and communication. Furthermore, we are interested in regulatory principles of transcriptional activation and protein turnover in the face of developmental processes or response to stress. We are therefore developing novel techniques to identify proteins that interact with regulatory domains in the genome, both in vivo and in vitro. In doing so, we aim to identify proteins that drive (or inhibit) transcription in a gene- and condition-specific manner, for example to understand how transcription of developmentally important genes is controlled. To further explore the link between genome regulation and protein output, we study protein turnover taking yeast as a model system. By determining protein synthesis and degradation proteome-wide and across a range of growth conditions, we aim to construct models of how protein homeostasis is maintained.

Future projects and goals

  • Develop new tools to study protein-DNA and protein-RNA interactions to identify and functionally characterise proteins that regulate transcription and translation.
  • Integration of proteomics and next-generation sequencing to understand the molecular basis of protein homeostasis.
  • Study cellular communication via secretory proteins.