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Plastoglobules proteome of maize

ABSTRACT: Despite the inherent difficulties in isolating PGs due to their lipid-rich nature and their tight association with thylakoid membranes, coupled with the absence of a robust, established protocol specifically for maize, we successfully adapted and significantly optimized the Arabidopsis thaliana PG isolation methodology. Our refined protocol involved initial isolation of intact chloroplasts from leaves, followed by ultrasonic disruption to release PGs and membrane fragments. Subsequently, the ultrasonically disrupted samples underwent two rounds of sucrose density gradient ultracentrifugation, yielding highly purified PGs. These purified PGs were then subjected to trypsin digestion and desalting, and the resulting peptides were analyzed by Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). Proteomics data were acquired using Data-Independent Acquisition (DIA) technology. This rigorous approach allowed us to obtain comprehensive PGs proteomic profiles from two biological replicates of B73 inbred line leaves.

ORGANISM(S): Zea Mays

SUBMITTER: Yongcai Huang

PROVIDER: PXD068249 | iProX | Wed Sep 10 00:00:00 BST 2025

REPOSITORIES: iProX

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Project 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.

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Plastoglobules proteome of maize

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