Dataset Information

Large-scale Perspective on Protein Dynamics in Tomato Fruit Tissues Development through Label-free Deep Shotgun Proteomics

ABSTRACT: Current innovations in mass-spectrometry-based technologies allow deep coverage of protein expression. Despite its immense value and in contrast to transcriptomics, only a handful of studies in Arabidopsis and especially other plant species engaged with global proteome assays. Here, we present large-scale protein profiling of tomato fruit across two key tissues and five developmental stages. This was accomplished by means of a shotgun proteomic assay comprising prior multi-step peptide fractionation followed by nano flow liquid chromatography coupled with high-resolution mass-spectrometry. A total of 7738 individual proteins were identified and reliably measured at least in one of the analysed tissues or stages. The detection of 115 putative transcription factors (TFs) further demonstrated the depth of our assay since a small number of TF proteins are typically detected in plant proteomics assays. Among this TFs set, 61 were differentially expressed in fruit development including renowned ripening regulators and elements of ethylene signalling. Curiously, we measured more than 80% of the predicted enzymatic reactions in the tomato metabolic network. Hence, proteins representing almost the complete set of reactions in major metabolic pathways were detected including the cytosolic and plastidic isoprenoid and the phenylpropanoid pathways. Furthermore, the data allowed us to discern between protein isoforms according to expression patterns which is most significant in light of the weak transcript-protein expression correspondence. Finally, visualization of changes in protein abundance associated with a particular process provided us with a unique, protein level view of skin and flesh tissues in developing fruit. This study adds a different perspective to the existing genomic, transcriptomic and metabolomic resources. It is therefore likely to promote translational and post-translational research in tomato and additional species which is presently focused on transcription.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Solanum Lycopersicum

SUBMITTER: Yishai Levin

LAB HEAD: Asaph Aharoni

PROVIDER: PXD004887 | Pride | 2017-01-30

REPOSITORIES: Pride

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Publications

Label-free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development.

Szymanski Jedrzej J Levin Yishai Y Savidor Alon A Breitel Dario D Chappell-Maor Louise L Heinig Uwe U Töpfer Nadine N Aharoni Asaph A

The Plant journal : for cell and molecular biology 20170322 2

Current innovations in mass-spectrometry-based technologies allow deep coverage of protein expression. Despite its immense value and in contrast to transcriptomics, only a handful of studies in crop plants engaged with global proteome assays. Here, we present large-scale shotgun proteomics profiling of tomato fruit across two key tissues and five developmental stages. A total of 7738 individual protein groups were identified and reliably measured at least in one of the analyzed tissues or stages ...[more]

PMID: 28112434

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Project description:Abscisic acid (ABA) regulates plant development and adaptation to environmental conditions. The ABA biosynthesis pathway in plants has been thoroughly elucidated; however, very few transcription factors directly regulating the expression of ABA biosynthetic genes have been identified. Here we show that the tomato (Solanum lycopersicum) zinc finger transcription factor SlZFP2, which is mainly expressed in developing fruits and axillary buds, negatively regulates ABA biosynthesis. Overexpression of SlZFP2 resulted in multiple phenotypic changes, including more branches, early flowering, delayed fruit ripening, lighter seeds and faster seed germination, whereas gene silencing by RNA interference (RNAi) caused poor fruit set and inhibited seed germination. Gene expression analysis showed that SlZFP2 represses ABA biosynthesis mainly through downregulation of the ABA biosynthetic genes SITIENS (SIT), FLACCA (FLC) and aldehyde oxidase SlAO1. SlZFP2 delays the onset of ripening through suppression of the ripening regulator COLORLESS NON-RIPENING (CNR). Using bacterial one hybrid screening and a selected amplification and binding assay we identified the (A/T)(G/C)TT repeat as the core binding sequence of SlZFP2. We further identified a large number of tomato genes containing putative SlZFP2 binding sites in their promoter regions. Chromatin immunoprecipitation and electrophoretic mobility shift assays demonstrated that SIT, FLC and SlAO1 are direct targets of SlZFP2 through binding to their promoter regions. We propose that SlZFP2 represents a novel negative regulator for fine tuning ABA biosynthesis during fruit development and provides a potentially valuable tool for dissecting the role of ABA in fruit ripening.To gain further insight on transcriptome changes regulated by SlZFP2, we sequenced a representative SlZFP2 RNAi line in LA1589 background and its nontransgenic sibling (WT) on a Miseq platform. The RNAi line 207 showed defected fruit set and ABA biosynthesis were chosen for profiling gene expression via RNA sequencing. Its nontransgenic sibling was served as controls. Three biological replicates were conducted.

Dataset Information

Large-scale Perspective on Protein Dynamics in Tomato Fruit Tissues Development through Label-free Deep Shotgun Proteomics

Publications

Label-free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development.

Similar Datasets

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