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.

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...

Despite its central role as the ark of genetic information and gene expression the plant nucleus is surprisingly understudied. We isolated nuclei from the Arabidopsis thaliana dark grown cell culture left untreated and treated with flg22 and nlp20, two elicitors of pattern triggered immunity (PTI) in plants, respectively. An liquid chromatography mass spectrometry (LC–MS) based discovery proteomics approach was used to measure the nuclear proteome fractions. An enrichment score based on the relative abundance of cytoplasmic, mitochondrial and Golgi markers in the nuclear protein fraction allowed us to curate the nuclear proteome producing high quality catalogs of around 3,000 nuclear proteins under untreated and both PTI conditions. The measurements also covered low abundant proteins including more than 100 transcription factors and transcriptional co-activators. We disclose a list of several hundred potentially dual targeted proteins including proteins not yet found before for further study. Protein import into the nucleus in plant immunity is known. Here we sought to gain a broader impression of this phenomenon employing our proteomics data and found 157 and 73 proteins to possibly be imported into the nucleus upon stimulus with flg22 and nlp20, respectively. Furthermore, the abundance of 93 proteins changed significantly in the nucleus following elicitation of immunity. These results suggest promiscuous ribosome assembly and a role of prohibitins and cytochrome C in the nucleus in PTI.

The mammalian intestine is a unique ecosystem for thousands of bacterial species and strains. How naturally coexisting bacteria of the microbiota interact with each other is not yet fully understood. Here, we isolated formerly coexisting, closely related strains of the genusBacteroidesfrom the intestines of healthy, wild-derived mice. The effect of one strain on another strain’s growth was tested in 169 pairsin vitro. We find a vast diversity of growth promoting and growth inhibiting activities. A strong positive effect was observed between two strains with differing metabolisms. Growth inhibition among a subset of strains was associated with the known bacterial toxin bacteroidetocin B. Across all strains, we observed growth promotion more often than growth inhibition. The effects were independent of two strains belonging to the same or different species. In some cases, one species differed in its effect on another according to host origin. These findings on obligate host-associated bacteria demonstrate that closely related and naturally coexisting strains have the potential to affect each other’s growth positively or negatively. These results have implications for our basic understanding of host-associated microbes and the design of synthetic microbial communities.

Despite its central role as the ark of genetic information and gene expression the plant nucleus is surprisingly understudied. We isolated nuclei from the Arabidopsis thaliana dark grown cell culture left untreated and treated with flg22 and nlp20, two elicitors of pattern triggered immunity (PTI) in plants, respectively. An LC-MS based discovery proteomics approach was used to measure the nuclear proteome fractions. An enrichment score based on the relative abundance of cytoplasmic, mitochondrial and golgi markers in the nuclear protein fraction allowed us to curate the nuclear proteome producing high quality catalogs of around 3,000 nuclear proteins under untreated and both PTI conditions. The measurements also covered low abundant proteins including more than 100 transcription factors and transcriptional co-activators. Protein import into the nucleus in plant immunity is known. Here we sought to gain a broader impression of this phenomenon employing our proteomics data and found 157 and 73 proteins to be putatively imported into the nucleus upon stimulus with flg22 and nlp20, respectively. Furthermore, the abundance of 93 proteins changed significantly in the nucleus following elicitation of immunity. These results suggest promiscuous ribosome assembly and retrograde signaling from the mitochondrion to the nucleus including Prohibitins and Cytochrome C, in the two forms of PTI.