About

Klaas van Wijk is a Professor in the Plant Biology Section at Cornell University, with a primary focus on chloroplast biology. His research involves understanding chloroplast proteostasis and function, including the study of plastoglobules, plastid differentiation, and proteomics related to chloroplasts. His passion is centered on chloroplast biology, and he dedicates his efforts to writing up research findings and securing funding for ongoing projects. As a leader in his field, he oversees a lab that investigates the molecular mechanisms governing chloroplast function, with particular attention to protease systems such as the Clp protease system in Arabidopsis. His work aims to elucidate the regulation of substrate delivery and degradation within chloroplasts, contributing to a deeper understanding of plant cell biology and proteostasis networks.

Research topics

• Biology
• Political Science
• Computer Science
• Sociology
• Computational biology
• Environmental science
• Biochemistry
• Cell biology
• Genetics
• Data science
• Ecology
• Environmental resource management
• Bioinformatics

Selected publications

• Structure, function, and substrates of Clp AAA+ protease systems in cyanobacteria, plastids, and apicoplasts: A comparative analysis

  Journal of Biological Chemistry · 2021 · 75 citations

  Senior authorCorresponding
  • Biology
  • Biochemistry
  • Cell biology

  ATPases Associated with diverse cellular Activities (AAA+) are a superfamily of proteins that typically assemble into hexameric rings. These proteins contain AAA+ domains with two canonical motifs (Walker A and B) that bind and hydrolyze ATP, allowing them to perform a wide variety of different functions. For example, AAA+ proteins play a prominent role in cellular proteostasis by controlling biogenesis, folding, trafficking, and degradation of proteins present within the cell. Several central proteolytic systems (e.g., Clp, Deg, FtsH, Lon, 26S proteasome) use AAA+ domains or AAA+ proteins to unfold protein substrates (using energy from ATP hydrolysis) to make them accessible for degradation. This allows AAA+ protease systems to degrade aggregates and large proteins, as well as smaller proteins, and feed them as linearized molecules into a protease chamber. This review provides an up-to-date and a comparative overview of the essential Clp AAA+ protease systems in Cyanobacteria (e.g., Synechocystis spp), plastids of photosynthetic eukaryotes (e.g., Arabidopsis, Chlamydomonas), and apicoplasts in the nonphotosynthetic apicomplexan pathogen Plasmodium falciparum. Recent progress and breakthroughs in identifying Clp protease structures, substrates, substrate adaptors (e.g., NblA/B, ClpS, ClpF), and degrons are highlighted. We comment on the physiological importance of Clp activity, including plastid biogenesis, proteostasis, the chloroplast Protein Unfolding Response, and metabolism, across these diverse lineages. Outstanding questions as well as research opportunities and priorities to better understand the essential role of Clp systems in cellular proteostasis are discussed.

  DOI

• The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource

  The Plant Cell · 2021 · 70 citations

  1st authorCorresponding
  • Biology
  • Computational biology
  • Bioinformatics

  We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana proteome, such as the significance of protein splice forms and post-translational modifications (PTMs), or simply to obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) data collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical, and biological metadata. Nearly 40 million out of ∼143 million MS/MS (tandem MS) spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17,858 uniquely identified proteins (only isoform per gene) at the highest confidence level (false discovery rate 0.0004; 2 non-nested peptides ≥9 amino acid each), assigned canonical proteins, and 3,543 lower-confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified that were generated from pseudogenes, alternative start, stops, and/or splice variants, and small Open Reading Frames; these features should be considered when updating the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB, and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS/MS data.

  DOI

• Vision, challenges and opportunities for a Plant Cell Atlas

  eLife · 2021 · 68 citations

  • Computer Science
  • Political Science
  • Data science

  Note: for full list of Plant Cell Atlas Consortium, see publication (p17). With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

  DOI

Recent grants

• A Hybrid Quadrupole Time-of-Flight Tandem Mass Spectrometer Integrated with UPLC for Characterization of Protein Complexes and Comparative Proteomics

  NSF · $349k · 2005–2008

• DETERMINATION OF THE N-DEGRON PATHWAY AND ITS SUBSTRATES IN PLANT CHLOROPLASTS

  NSF · $950k · 2023–2027

• CLPS1-CLPF ADAPTORS FOR PROTEASE SUBSTRATE SELECTION IN CHLOROPLASTS

  NSF · $930k · 2020–2024

• From Proplastid to Chloroplast: Understanding Plastid Differentiation in Maize through Microarray and Proteome Analysis

  NSF · $3.8M · 2002–2008

• Selection and Delivery of Substrates to the Essential Clp Protease Complex in Plastids of Arabidopsis Thaliana

  NSF · $798k · 2010–2014

Frequent coauthors

• Giulia Friso

  Cornell University

  49 shared

• Qi Sun

  Cornell University

  33 shared

• Lalit Ponnala

  19 shared

• A. Jimmy Ytterberg

  Uppsala University

  16 shared

• Wojciech Majeran

  Institut des Sciences des Plantes de Paris Saclay

  16 shared

• Eric W. Deutsch

  InSysBio (Russia)

  13 shared

• Vlad Zabrouskov

  Thermo Fisher Scientific (United States)

  13 shared

• Zhi Sun

  InSysBio (Russia)

  12 shared

Labs

• van Wijk LabPI

Education

• B.S.

  Agricultural University Wageningen

• M.S.

  Agricultural University Wageningen

• Ph.D.

  University of Groningen

Awards & honors

• Research Award from the Alexander von Humboldt Foundation (2…
• Humboldt Foundation Guest research summer fellowship (2009)
• WennerGren Foundation, Stockholm, Sweden
• Roger E. Koeppe Lecture (2006)
• Melvin Calvin Award (2004)

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