Reshaping of the Arabidopsis thaliana Proteome Landscape and Co-regulation of Proteins in Development and Immunity

Abstract

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 agespecific 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.

LC-MS Based Draft Map of theArabidopsis thalianaNuclear Proteome and Protein Import in Pattern Triggered Immunity

“…This was particularly pronounced following elicitation of PTI by flg22 (Figure 3C right panel). It has been reported by us and others (see Bassal 2020 for citations) (Bassal et al, 2020) that ribosome composition is promiscuous dependent on cellular state and our result imply the same in the context of ribosome assembly in the nucleus. Finally, the abundance of another protein of interest to us, phospholipase D alpha 1 also increased significantly following stimulus of protoplasts with either flg22 or nlp20.…”

Cost-effective circadian mechanism: rhythmic degradation of circadian proteins spontaneously emerges without rhythmic post-translational regulation

“… Bassal et al, 2020 ; Brennan et al., 2013 ; Kulak et al., 2014 ; Narumi et al, 2016 ; Pierce et al., 2009 .…”

Does Filter Aided Sample Preparation (FASP) Provide Sufficient Method Linearity for Quantitative Plant Shotgun Proteomics?

“…Protein isolation relied on two approaches: (i) the phenol extraction method described in detail previously 17 and (ii) treatment with an SDS-based solution according to the procedure recently described by Bassal et al 18 with minor modifications. In detail, protein isolation from PC-3 cells and a mixture of pea seed powder and Arabidopsis leaf material was accomplished by treatment with extraction buffer (4% (w/v) SDS, 10 mmol/L dithiothreitol (DTT), 10 mmol/L EDTA, 1 mmol/L PMSF in 50 mmol/L Tris-HCl, pH 8.0), followed by two steps of incubation (900 rpm; at 95°C for 10 min, at room temperature for 20 min) and centrifugation (25 000 g, 30 min, 10°C) after each incubation.…”