PXD006708

PXD006708 is an original dataset announced via ProteomeXchange.

Title	The transcriptome, extracellular proteome and active secretome of agroinfiltrated N. benthamiana uncover an expanded protease repertoire
Description	Background: The infiltration of disarmed Agrobacterium tumefaciens into leaves of Nicotiana benthamiana (agroinfiltration) is a widely-adopted procedure to produce and study proteins in plant science, for instance to determine subcellular localization and protein-protein interactions. Agroinfiltration also facilitates quick and safe production of biopharmaceuticals. However, the agroinfiltration expression platform is hampered by unintended proteolysis, some of which might be associated with an elevated immune response. Results: Here, we studied the transcriptome, extracellular proteome and active secretome of agroinfiltrated leaves over a time course, with and without the p19 silencing inhibitor. Remarkably, p19 expression had little effect on the leaf transcriptome and no effect on the extracellular proteome. 25% of the detected transcripts changed in abundance upon agroinfiltration, associated with a gradual upregulation of immunity and a downregulation of photosynthesis. By contrast, 70% of the extracellular proteins increase in abundance and for some proteins this coincides with increased efficiency of extracellular delivery. The protease repertoire of N. benthamiana is expanded compared to other model plants and consists of 1245 proteases and protease homologs. We detect transcripts encoding for 975 proteases, identified extracellular peptides from 196 proteases and monitored 17 active extracellular Ser and Cys proteases in agroinfiltrated leaves. Conclusions: Analysis of agroinfiltrated leaves at transcript, protein and activity levels uncover transcriptional and post-transcriptional/translational reprogramming upon agroinfiltration, associated with substantial increase of the extracellular proteome, and a complex, expanded protease repertoire. This dataset increases our understanding of the plant response to agroinfiltration and indicates ways to improve a key expression platform for both plant science and molecular farming.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_02:27:08.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Farnusch Kaschani
SpeciesList	scientific name: Nicotiana benthamiana; NCBI TaxID: 4100; scientific name: Agrobacterium fabrum str. C58; NCBI TaxID: 176299;
ModificationList	carbamoylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2017-06-13 23:43:35	ID requested
⏵ 1	2017-10-24 02:27:09	announced

Grosse-Holz F, Kelly S, Blaskowski S, Kaschani F, Kaiser M, van der Hoorn RAL, The transcriptome, extracellular proteome and active secretome of agroinfiltrated Nicotiana benthamiana uncover a large, diverse protease repertoire. Plant Biotechnol J, 16(5):1068-1084(2018) [pubmed]

curator keyword: Biological

submitter keyword: agroinfiltration, extracellular proteome, Nicotiana benthamiana, Agrobacterium tumefaciens, plant immunity, plant protease annotation, plant protease family, RNAseq, activity-based protein profiling (ABPP), activity-based proteomics, silencing inhibitor p19, chlorosis, post-translational activation

Farnusch Kaschani
contact affiliation	Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany
contact email	farnusch.kaschani@uni-due.de
lab head
Farnusch Kaschani
contact affiliation	University Duisburg-Essen
contact email	farnusch.kaschani@uni-due.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD006708
     1. Label: PRIDE project
     2. Name: The transcriptome, extracellular proteome and active secretome of agroinfiltrated N. benthamiana uncover an expanded protease repertoire