Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

Jelle van Leene (1) , Jens Hollunder (1) , Dominique Eeckhout (1) , Geert Persiau (1) , Eveline van de Slijke (1) , Hilde Stals (1) , Gert van Isterdael (1) , Aurine Verkest (1) , Sandy Neirynck (1) , Yelle Buffel (1) , Stefanie de Bodt (1) , Steven Maere (1) , Kris Laukens (2) , Anne Pharazyn (3) , Paulo C G Ferreira (4) , Nubia Eloy (1, 4) , Charlotte Renne (5) , Christian Meyer (5) , Jean Denis Faure (5) , Jens Steinbrenner (6) , Jim Beynon (6) , John C Larkin (7) , Yves van de Peer (1) , Pierre Hilson (8) , Martin Kuiper (1) , Lieven de Veylder (1) , Harry van Onckelen (3) , Dirk Inze (1) , Erwin Witters (3, 9) , Geert de Jaeger (1)

1 Department of Plant Systems Biology, Department of Plant Biotechnology and Genetics
2 Department of Mathematics and Computer Science
3 Center for Proteome Analysis and Mass Spectrometry, Department of Biology
4 Instituto de Bioquímica Médica, Centro de Ciências da Saúde
5 IJPB - Institut Jean-Pierre Bourgin
6 School of Life Sciences
7 Department of Biological Sciences
8 Department of Plant Systems Biology - Department of Plant Biotechnology and Genetics
9 VITO - Flemish Institute for Technological Research

Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up-and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)-cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A-and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA; 1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK-cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants. Molecular Systems Biology 6: 397; published online 10 August 2010; doi:10.1038/msb.2010.53 Subject Categories: plant biology; metabolic & regulatory networks

Mots clés: cell cycle; interactome; protein complex; protein interactions; tandem affinity purification; protein-protein interactions; anaphase-promoting complex; plant-systems biology; genome-wide analysis; dependent kinase; dna-replication; gene ontology; expression

Domaines: Sciences du Vivant [q-bio]

Jelle van Leene, Jens Hollunder, Dominique Eeckhout, Geert Persiau, Eveline van de Slijke, et al.. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Molecular Systems Biology, 2010, 6, pp.397. ⟨10.1038/msb.2010.53⟩. ⟨hal-01203927⟩