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Diurnal Dynamics of the Arabidopsis Rosette Proteome and Phosphoproteome

View ORCID ProfileR. Glen Uhrig, Sira Echevarría-Zomeño, Pascal Schlapfer, View ORCID ProfileJonas Grossmann, View ORCID ProfileBernd Roschitzki, Niklas Koerber, View ORCID ProfileFabio Fiorani, View ORCID ProfileWilhelm Gruissem
doi: https://doi.org/10.1101/2020.09.11.293779
R. Glen Uhrig
1Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
4Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Sira Echevarría-Zomeño
1Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
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Pascal Schlapfer
1Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
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Jonas Grossmann
2Functional Genomics Center Zurich, University of Zurich, 8057 Zurich, Switzerland
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Bernd Roschitzki
2Functional Genomics Center Zurich, University of Zurich, 8057 Zurich, Switzerland
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Niklas Koerber
3Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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Fabio Fiorani
3Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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Wilhelm Gruissem
1Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
5Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
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  • For correspondence: wgruissem@ethz.ch
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ABSTRACT

Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional regulation controls diurnal fluctuations at the protein-level. Here we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 h light : 12 h dark diurnal cycle and the phosphoproteome immediately before and after the light-to-dark and dark-to-light transitions. We quantified nearly 5000 proteins and 800 phosphoproteins, of which 288 fluctuated in their abundance and 226 fluctuated in their phosphorylation status. Of the phosphoproteins, 60% were quantified for changes in protein abundance. This revealed six proteins involved in nitrogen and hormone metabolism that had concurrent changes in both protein abundance and phosphorylation status. The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. The phosphoproteome at the light-dark transitions revealed the dynamics at phosphorylation sites in either anticipation of or response to a change in light regime. Phosphorylation site motif analyses implicate casein kinase II and calcium/calmodulin dependent kinases among the primary light-dark transition kinases. The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant.

Summary Statement The manuscript provides quantitative information of diurnal changes in the accumulation and phosphorylation of proteins in Arabidopsis thaliana rosettes grown in a 12 h photoperiod. The highly resolved time-scale of the datasets offer new proteome-level insights for future targeted studies.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Funding: This work was funded by TiMet - Linking the Clock to Metabolism (Grant Agreement 245143) supported by the European Commission (FP7-KBBE-2009-3). Experiments conducted at Forschungszentrum Jülich were partly funded by the Helmholtz Association.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted September 12, 2020.
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Diurnal Dynamics of the Arabidopsis Rosette Proteome and Phosphoproteome
R. Glen Uhrig, Sira Echevarría-Zomeño, Pascal Schlapfer, Jonas Grossmann, Bernd Roschitzki, Niklas Koerber, Fabio Fiorani, Wilhelm Gruissem
bioRxiv 2020.09.11.293779; doi: https://doi.org/10.1101/2020.09.11.293779
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Diurnal Dynamics of the Arabidopsis Rosette Proteome and Phosphoproteome
R. Glen Uhrig, Sira Echevarría-Zomeño, Pascal Schlapfer, Jonas Grossmann, Bernd Roschitzki, Niklas Koerber, Fabio Fiorani, Wilhelm Gruissem
bioRxiv 2020.09.11.293779; doi: https://doi.org/10.1101/2020.09.11.293779

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