Dataset Information

Phloem proteomics in Arabidopsis thaliana: identification of small peptides

ABSTRACT: The objective of this study is to analyse the protein composition of A. thaliana phloem at different stages of development. For this purpose phloem exudates have been collected at different time points (vegetative stage, floral transition and reproductive stage).

INSTRUMENT(S):

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

TISSUE(S): Phloem

SUBMITTER: Reyes Benlloch Ortiz

LAB HEAD: Reyes Benlloch Ortiz

PROVIDER: PXD065325 | Pride | 2026-04-13

REPOSITORIES: Pride

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Publications

Phloem Proteomics to Identify Small Open Reading Frame (sORF)-encoded Peptides With a Putative Role in the Control of Flowering Time in Arabidopsis.

Moreno-Sanguino Irene I Collás Lucía Argente LA Samuelsson Göran G Wingsle Gunnar G Benlloch Reyes R

Physiologia plantarum 20260301 2

Phloem sap proteomic studies have previously revealed that phloem sap composition varies during development and upon floral induction. Specific proteins, lipids, messenger RNAs (mRNAs), and peptides have been shown to accumulate at different developmental stages. Peptides are of special interest since they have the potential to act as regulatory molecules controlling plant responses to environmental changes, such as salinity and water stress, plant-microbe interactions, and developmental changes ...[more]

PMID: 41937606

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Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Cucurbita maxima tissues (including leaves, flowers and phloem sap). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, flowers and phloem sap of Cucurbita maxima, variety Big Max. Total RNA was isolated using the TriReagent (Molecular Research Center) for leaves and phloem sap and the Plant RNA Purification Reagent (Invitrogen) for flowers, and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Pamela Green for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

Project description:Phloem is the primary conduit through which photosynthates, hormones, and other biologically important molecules are distributed from aerial plant organs downward and throughout the plant. Increasing evidence suggests that phloem contents are diverse and play a critical role in biotic and abiotic stress adaptation. Drought causes the greatest decreases in agricultural crop productivity among all biotic and abiotic stresses, and the link between water deficiency and phloem protein contents is relatively unexplored. Here we employed the EDTA-facilitated phloem exudate collection method from Solanum lycopersicum leaves during a period of drought stress and recovery. Our analysis resulted in the confident identification and quantification of 2,558 proteins. Comparing our data with previous findings confirms that our exudate collection strategy enriched for known phloem proteins. Independent of drought, enrichment analysis of the total phloem exudate protein profiles from all samples suggest that the exchange of proteins into the phloem is more complex than previously thought, including additional protein chaperone systems, branched-chain amino acid synthesis proteins, trehalose metabolism, and RNA silencing proteins. During the experiment we observed 169 proteins whose abundance changed significantly within the phloem sap, the majority of which were impacted specifically in response to drought. Among these were proteins involved in lipid metabolism, chaperone-mediated protein folding, carboxylic acid metabolism, abscisic acid signaling, cytokinin biosynthesis, and amino acid metabolism are significantly upregulated during drought. Conversely, proteins involved in lipid signaling, sphingolipid metabolism, cell wall organization, carbohydrate metabolism, and a mitogen-activated protein kinase are downregulated in response to drought. Many of these observations are consistent with previous literature findings at the whole plant level but have not been localized to the vasculature in tomato, suggesting phloem plays a critical role in adaptation to drought stress in tomato .

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