PXD035944-3

PXD035944 is an original dataset announced via ProteomeXchange.

Title	The tomato chloroplast stromal proteome compendium elucidated by leveraging a plastid protein-localization prediction Atlas
Description	Tomato (Solanum lycopersicum) is a model species for studying fruit development, wounding, herbivory, and pathogen attack. Despite tomato’s world-wide economic importance and the role of chloroplasts as metabolic hubs and integrators of environmental cues, little is known about the stromal proteome of tomato. Using a high-yielding protocol for chloroplast and stromal protein isolation, MudPIT nano-LC-MS/MS analyses, a robust in-house protein database (the Atlas) for predicting the plastid localization of tomato proteins, and rigorous selection criteria for inclusion/exclusion in the stromal proteome, we identified 1,254 proteins of the tomato stromal proteome. We provide one of the most robust stromal proteomes available to date with empirical evidence for 550 and 105 proteins not previously described for tomato plastids and the Arabidopsis stroma, respectively. The relative abundance of tomato stromal proteins was determined using the exponentially modified protein abundance index (emPAI). Comparison of the abundance of tomato and Arabidopsis stromal proteomes provided evidence for the species-specific nature of stromal protein homeostasis. The manual curation of the tomato stromal proteome classified proteins into ten functional categories resulting in an accessible compendium of tomato chloroplast proteins. After curation, only 88 proteins remained as unknown, uncharacterized or as enzymes with unknown functions. The curation of the tomato stromal proteins also indicated that tomato has a number of paralogous proteins, not present in Arabidopsis, which accumulated to different levels in chloroplasts. As some of these proteins function in key metabolic pathways or in perceiving or transmitting signals critical for plant adaptation to biotic and abiotic stress, these data suggest that tomato may modulate the bidirectional communication between chloroplasts and nuclei in a novel manner. The stromal proteome provides a fertile ground for future mechanistic studies in the field of tomato chloroplast-nuclear signaling and are foundational for our goal of elucidating the dynamics of the stromal proteome controlled by the solanaceous-specific, stromal, and wound-inducible leucine aminopeptidase A of tomato.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:09:43.206.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Linda Walling
SpeciesList	scientific name: Solanum lycopersicum; NCBI TaxID: 4081;
ModificationList	acetylated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-08-10 09:20:37	ID requested
1	2023-10-24 12:23:59	announced
2	2023-11-14 09:09:43	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 06:09:46	announced	2024-10-22: Updated project metadata.

Bhattacharya O, Ortiz I, Hendricks N, Walling LL, The tomato chloroplast stromal proteome compendium elucidated by leveraging a plastid protein-localization prediction Atlas. Front Plant Sci, 14():1020275(2023) [pubmed]

10.3389/fpls.2023.1020275;

submitter keyword: lumenal proteins, protein homeostasis, proteomics,chloroplast, Solanum lycopersicum, redox, leucine aminopeptidase, stroma

Linda L. Walling
contact affiliation	University of California, Riverside
contact email	lwalling@ucr.edu
lab head
Linda Walling
contact affiliation	Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
contact email	lwalling@ucr.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/10/PXD035944

PRIDE project URI

• PRIDE
  1. PXD035944
     1. Label: PRIDE project
     2. Name: The tomato chloroplast stromal proteome compendium elucidated by leveraging a plastid protein-localization prediction Atlas