Reshaping of theArabidopsis thalianaproteome landscape and co-regulation of proteins in development and immunity

Abstract

24Proteome remodeling is a fundamental adaptive response and proteins in complex and 25 functionally related proteins are often co-expressed. Using a deep sampling strategy we 26 define Arabidopsis thaliana tissue core proteomes at around 10,000 proteins per tissue 27 and absolutely quantify (copy numbers per cell) nearly 16,000 proteins throughout the 28 plant lifecycle. A proteome wide survey of global post translational modification revealed 29 amino acid exchanges pointing to potential conservation of translational infidelity in 30 eukaryotes. Correlation analysis of protein abundance uncovered potentially new tissue 31 and age specific roles of entire signaling modules regulating transcription in 32 photosynthesis, seed development and senescence and abscission. Among others, the 33 data suggest a potential function of RD26 and other NAC transcription factors in seed 34 development related to desiccation tolerance as well as a possible function of Cysteine-35 rich Receptor-like Kinases (CRKs) as ROS sensors in senescence. All of the 36 components of ribosome biogenesis factor (RBF) complexes were co-expressed tissue 37 and age specifically indicating functional promiscuity in the assembly of these little 38 described protein complexes in Arabidopsis. Treatment of seedlings with flg22 for 16 39 hours allowed us to characterize proteome architecture in basal immunity in detail. The 40 results were complemented with parallel reaction monitoring (PRM) targeted 41 proteomics, phytohormone, amino acid and transcript measurements. We obtained 42 strong evidence of suppression of jasmonate (JA) and JA-Ile levels by deconjugation 43 and hydroxylation via IAA-ALA RESISTANT3 (IAR3) and JASMONATE-INDUCED 44 OXYGENASE 2 (JOX2) under the control of JASMONATE INSENSITIVE 1 (MYC2). 45 This previously unknown regulatory switch is another part of the puzzle of the as yet 46 understudied role of JA in pattern triggered immunity. The extensive coverage of the 47 Arabidopsis proteome in various biological scenarios presents a rich resource to plant 48 biologists that we make available to the community.49 50 51 52 53 Proteome biology is receiving increasing interest in the last years but still proves difficult 54 on a genome wide scale in plants. The proteome is the most fundamental active 55 determinant of an organism's phenotype and its landscape is large, complex and 56 dynamic, entailing changes in protein abundance, interaction, post translational 57 modification (PTM) and sub-cellular localization. 58 Steady state protein abundance at a certain time point is to a considerable part 59 determined by the abundance of its transcript and the latter's translation rate. Synthesis 60 is however only half of the equation governing protein abundance, indeed Arabidopsis 61 has more than 600 F-box proteins as components of diverse E3 ubiquitin ligase 62 complexes that direct protein degradation. Newer evidence has shown that post 63 transcriptional and translational mechanisms (Ponnala et al., 2014; Merchante et al., 64 2017) and...

A NYN domain protein directly interacts with DECAPPING1 and is required for phyllotactic pattern

“…Our study of proteins associated with DCP1, DCP2 and DNE1 is more in favor of the second hypothesis and suggests the existence in plants, of a protein complex based on DCP1-DNE1 in parallel of the canonical decapping complex based on DCP1-DCP2. Comparing DCP1, DCP2 and DNE1 protein copies per cell (pcc) as found in a recent global proteomic analysis (Bassal et al, 2020) reveal that DCP1 is the more abundant protein (234128 pcc) followed by DCP2 (67345 pcc) and finally DNE1 (791 pcc). This data supports the existence of a main complex containing DCP2 and of an accessory complex containing DNE1.…”

Multilayer regulatory landscape during pattern‐triggered immunity in rice

“…Previous studies have applied single or dual omics to uncover the molecular mechanisms involved in plant–pathogen interactions (Bassal et al ., 2020; Bjornson et al ., 2021; Chen et al ., 2018; Jeon et al ., 2020; Lovelace et al ., 2018; Nobori et al ., 2018, 2020; Winkelmüller et al ., 2021). In this study, we performed a multi‐omics analysis consisting of five omics datasets including metabolome, transcriptome, proteome, ubiquitome and acetylome to systematically elucidate PTI triggered by two different PAMPs in rice.…”

“…Like in Arabidopsis , similar PTI‐mediated defence occurs in rice against fungal and bacterial infection, such as ROS production, callose deposition, MAPK signalling cascade activation and the hormone signalling pathways activation (Liu et al ., 2013, 2014; Yang et al ., 2013). Up to now, some single or combined omics studies, including transcriptomic, proteomics and metabolomics, have been reported to investigate the effects of plant responses to invading pathogens or challenged by different PAMPs (Bassal et al ., 2020; Bjornson et al ., 2021; Chen et al ., 2018; Jeon et al ., 2020; Lovelace et al ., 2018; Nobori et al ., 2018; Winkelmüller et al ., 2021). However, an integrative study of multi‐omics data is still lacking.…”

The Lys‐motif receptor LYK4 mediates Enterobacter sp. SA187 triggered salt tolerance in Arabidopsis thaliana

“…CRKs belong to a large gene family of receptors, but several play important roles in plant defence and immunity (Wrzaczek et al ., 2010). Among these, differential regulation in LYK4 mutants was found for CRK8 , which may act as ROS sensors (Bassal et al ., 2020) as well as CRK9 , which plays a redundant function with CRK4 and CRK5 in ABA signalling (Lu et al ., 2016). The differential regulation of several regulators of MAPK signalling, such as PUB23 and PUB24 (Trujillo et al ., 2008), and MAPK targets, such as WRKY48 (Xing et al ., 2008) and WRKY53 (Wan et al ., 2004), substantiate that LYK4 plays an important role in regulating defence reactions during SA187–Arabidopsis interaction.…”