Dataset Information

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 complex and functionally related proteins are often co-expressed. Using a deep sampling strategy we define Arabidopsis thaliana tissue core proteomes at 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. The deep proteome data is available from PRIDE submission PXD019330. Those results were complemented in this submission with parallel reaction monitoring (PRM) targeted proteomics over 1, 3 and 16 hours of flg22 exposure. The extensive coverage of the Arabidopsis proteome in various biological scenarios presents a rich resource to plant biologists that we make available to the community.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

SUBMITTER: Steffen Neumann

LAB HEAD: Wolfgang Hoehenwarter

PROVIDER: PXD021753 | Pride | 2020-10-02

REPOSITORIES: Pride

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

Bassal Mona M Abukhalaf Mohammad M Majovsky Petra P Thieme Domenika D Herr Tobias T Ayash Mohamed M Tabassum Naheed N Al Shweiki Mhd Rami MR Proksch Carsten C Hmedat Ali A Ziegler Jörg J Lee Justin J Neumann Steffen S Hoehenwarter Wolfgang W

Molecular plant 20200929 12

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 ...[more]

PMID: 33007468

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Project description:Plants have evolved strong innate immunity mechanisms, but successful pathogens evade or suppress plant immunity via effectors delivered into the plant cell. Hyaloperonospora arabidopsidis (Hpa) causes downy mildew on Arabidopsis thaliana, and a genome sequence is available for isolate Emoy2. Here, we exploit the availability of genome sequences for Hpa and Arabidopsis to measure gene-expression changes in both Hpa and Arabidopsis simultaneously during infection. Using a high-throughput cDNA tag sequencing method, we reveal expression patterns of Hpa predicted effectors and Arabidopsis genes in compatible and incompatible interactions, and promoter elements associated with Hpa genes expressed during infection. By resequencing Hpa isolate Waco9, we found it evades Arabidopsis resistance gene RPP1 through deletion of the cognate recognized effector ATR1. Arabidopsis salicylic acid (SA)-responsive genes including PR1 were activated not only at early time points in the incompatible interaction but also at late time points in the compatible interaction. By histochemical analysis, we found that Hpa suppresses SA-inducible PR1 expression, specifically in the haustoriated cells into which host-translocated effectors are delivered, but not in non-haustoriated adjacent cells. Finally, we found a highly-expressed Hpa effector candidate that suppresses responsiveness to SA. As this approach can be easily applied to host-pathogen interactions for which both host and pathogen genome sequences are available, this work opens the door towards transcriptome studies in infection biology that should help unravel pathogen infection strategies and the mechanisms by which host defense responses are overcome. Three weeks old Arabidopsis (Col-0) plants were inoculated with either the avirulent isolate Emoy2 (incompatible interaction) or the virulent isolate Waco9 (compatible interaction) of Hpa, and infected plants were harvested at 1, 3 and 5 days post-inoculation (dpi) for total RNA extraction. mRNA profiles were generated by deep sequencing on Illumina GAIIx using EXPRSS tag-seq protocol. Each biological replicate set of samples were sequenced as one batch (biorep1, biorep2 and biorep3 in filenames) and each batch was sequenced in 4 individual Illumina flowcell lanes (lane1 to lane4 in filenames). Four sequecing lanes of each three biological repliates resulted in 12 sequencing libraries. Emoy2 1, 3 and 5 dpi samples and Waco9 1 dpi samples were made two different codes (lib1 and lib2 in filenames) to generate higher depth of sequencing data. Each biological replicate set of samples were sequenced as one batch and each batch was sequenced in 4 individual Illumina flowcell lanes. Four sequecing lanes of each three biological repliates resulted in 12 sequencing libraries. 'The unassigned read_*' samples are for 'nobarcode_biorep[x]_lanne[x].fq' file containing sequences unassigned to any barcode from respective bioreplicate sequencing lanes.

			Action	DRS
	Control_flg22_1316hrs.csv	Csv
	Control_flg22_1316hrs_IAR3.csv	Csv
	Control_flg22_16hrs_150519.csv	Csv
	ISA-Tab.zip	Other
	MAK130320_C-1.raw	Raw