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Bassal, M.; Abukhalaf, M.; Majovsky, P.; Thieme, D.; Herr, T.; Ayash, M.; Tabassum, N.; Al Shweiki, M. R.; Proksch, C.; Hmedat, A.; Ziegler, J.; Lee, J.; Neumann, S.; Hoehenwarter, W.; Reshaping of the Arabidopsis thaliana Proteome Landscape and Co-regulation of Proteins in Development and Immunity Mol. Plant 13, 1709-1732, (2020) DOI: 10.1016/j.molp.2020.09.024
Proteome remodeling is a fundamental adaptive response, and proteins in
complexes and functionally related proteins are often co-expressed.
Using a deep sampling strategy we define core proteomes of Arabidopsis thaliana
tissues with around 10 000 proteins per tissue, and absolutely quantify
(copy numbers per cell) nearly 16 000 proteins throughout the plant
lifecycle. A proteome-wide survey of global post-translational
modification revealed amino acid exchanges pointing to potential
conservation of translational infidelity in eukaryotes. Correlation
analysis of protein abundance uncovered potentially new tissue- and
age-specific roles of entire signaling modules regulating transcription
in photosynthesis, seed development, and senescence and abscission.
Among others, the data suggest a potential function of RD26 and other
NAC transcription factors in seed development related to desiccation
tolerance as well as a possible function of cysteine-rich receptor-like
kinases (CRKs) as ROS sensors in senescence. All of the components of
ribosome biogenesis factor (RBF) complexes were found to be co-expressed
in a tissue- and age-specific manner, indicating functional promiscuity
in the assembly of these less-studied protein complexes in Arabidopsis. Furthermore, we characterized detailed proteome remodeling in basal immunity by treating Arabidopsis
seeldings with flg22. Through simultaneously monitoring
phytohormone and transcript changes upon flg22 treatment, we obtained
strong evidence of suppression of jasmonate (JA) and JA-isoleucine
(JA-Ile) levels by deconjugation and hydroxylation by IAA-ALA RESISTANT3
(IAR3) and JASMONATE-INDUCED OXYGENASE 2 (JOX2), respectively, under
the control of JASMONATE INSENSITIVE 1 (MYC2), suggesting an
unrecognized role of a new JA regulatory switch in pattern-triggered
immunity. Taken together, the datasets generated in this study present
extensive coverage of the Arabidopsis proteome in various biological scenarios, providing a rich resource available to the whole plant science community.