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The small RNA component of Arabidopsis phloem sap and its response to iron deficiency.

ABSTRACT: The small RNA component of Arabidopsis phloem sap and its response to iron deficiency.

PROVIDER: PRJNA925510 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23126039.fastq.gz	Fastqsanger.gz
	SRR23126040.fastq.gz	Fastqsanger.gz
	SRR23126041.fastq.gz	Fastqsanger.gz
	SRR23126042.fastq.gz	Fastqsanger.gz
	SRR23126043.fastq.gz	Fastqsanger.gz

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The small RNA component of Arabidopsis phloem sap and its response to iron deficiency.

Project description:We performed small RNA-seq (sRNA-seq) study of Arabidopsis phloem sap under iron-sufficient (+Fe; control) and iron deficient (-Fe) conditions to investigate and identify sRNAs whose expression is regulated by iron deficiency in the phloem sap.

2023-08-08 | GSE223278 | GEO

Deciphering phloem sap protein composition to unravel long distance signaling in iron deficiency growth conditions.Deciphering phloem sap protein composition to unravel long distance signaling in iron deficiency growth conditions.

Project description:To get further insights into the potential involvement of proteins in long distance signaling of leaves iron status to the root system, a label free experiment was done to determine the protein phloem sap composition in contrasted iron growth conditions in wild type and knock out Arabidopsis mutant of the master regulator gene URI (i.e., bhlh121).

2025-06-30 | PXD061925 | Pride

Small RNAs in different tissues and phloem of oilseed rape under nutrient stress conditions

Project description:The objective of this study was to identify nutrient-responsive small RNAs in different tissues and in phloem sap of rape plants. miRNA microarrays containing all currently known plant miRNAs (Sanger miRBase versions 10.0, 10.1 and 11.0), and a set of unknown small RNAs cloned earlier from Brassica phloem sap (Bn_PsRNA) were used. The phloem, leaf and root response to nutrient deficiency were analyzed by removing either sulfate, copper or iron from the growth medium. The small RNA profile from phloem and inflorescence stems of plants grown under full nutrition conditions was also analyzed and compared. The study demonstrates that the phloem sap sRNA profile is distinct from that of the inflorescence stems, leaves and roots. Furthermore, we could identify phloem-enriched small RNAs and showed that some of them specifically accumulate in the phloem in response to nutrient deprivation.

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Phloem sap extracellular vesicles carry active proteasomes that increase in response to aphid infestation

Project description:The morphogenesis of higher plants requires communication among distant organs throughout vascular tissues (xylem and phloem). Numerous investigations have demonstrated that phloem also act as a distribution route for signalling molecules being observed that different macromolecules translocated by the sap, including nucleic acids and proteins, change under stress situations. The participation of extracellular vesicles (EVs) in this communication has been suggested, although little is known about their role. In fact, in the last decade, the presence of EVs in plants has originated a great controversy, where major concerns arose from their origin, isolation methods, and even the appropriate nomenclature for plant nanovesicles.

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The Small RNA Component of <i>Arabidopsis thaliana</i> Phloem Sap and Its Response to Iron Deficiency.

Project description:In order to discover sRNA that might function during iron deficiency stress, RNA was prepared from phloem exudates of Arabidopsis thaliana, and used for RNA-seq. Bioanalyzer results indicate that abundant RNA from phloem is small in size-less than 200 nt. Moreover, typical rRNA bands were not observed. Sequencing of eight independent phloem RNA samples indicated that tRNA-derived fragments, specifically 5' tRFs and 5' tRNA halves, are highly abundant in phloem sap, comprising about 46% of all reads. In addition, a set of miRNAs that are present in phloem sap was defined, and several miRNAs and sRNAs were identified that are differentially expressed during iron deficiency.

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Transcriptome analysis of the Arabidopsis phloem

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Transcription profiling of Arabidopsis phloem

Project description:This sudy focuses on the identification of transcripts in the shoot phloem of the model plant Arabidopsis thaliana. Transcripts expressed in the phloem tissue (parenchyma cell, companion cell, sieve element) were excised by laser microdissection pressure catapulting (LMPC). These were compared with transcripts isolated from leaf phloem exudates by EDTA-chelation technique. Optimization of sample harvest resulted in RNA of high quality from both sources. Modifications of the RNA amplification procedure obtained RNA of sufficient yield and quality for microarray experiments. Microarrays (Affymetrix, ATH1) hybridized with RNA derived from phloem tissue by LMPC or phloem sap allowed us to differentiate between phloem located and mobile transcript species. The datasets provide a search criterion for phloem-based signals and will facilitate reverse genetic studies and forward genetic screens for phloem and long distance RNA signaling mutants. Experiment Overall Design: Arabidopsis plants were cultivated under short day conditions (8 h light) until flowering. Phloem tissue was isolated by Lasermicrodissection and Pressure Catapulting (LMPC) and phloem exudate by EDTA-chelation technique. In both experiments poly-A-RNA was extracted and amplified before hybridization of microarrays (Affymetrix, ATH1). For both experiments three LMPC-derived phloem tissue (LMPC-derived phloem_1-3) and three phloem exudate samples (Phloem exudate_1-3) were analysed. Precise protocols of plant growth, sample harvest, RNA extraction and amplification are provided in Deeken et al., 2008.

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Transcriptional analysis of phloem-associated cells of potato

Project description:To better understand the function of the phloem in plants, we have combined laser capture microdissection (LCM) and RNA-seq for an in-depth transcriptional profile of phloem-associated cells of both petioles and stems of potato. Out of the 27k transcripts assembled that we identified, approximately 15K were present in phloem-associated cells of petiole and stem with greater than ten reads. Approximately 22% of the transcripts in phloem cells contained at least one binding motif for Pumilio, Nova, or polypyrimidine tract-binding proteins in their downstream sequences. Highlighting the predominance of binding processes identified in the gene ontology analysis of active genes from phloem cells, 78% of the 464 RNA-binding proteins present in the potato genome were detected in our phloem transcriptome. As a reasonable alternative when phloem sap collection is not possible, LCM can be used to isolate RNA from specific cell types, and along with RNA-seq, provides practical access to expression profiles of phloem tissue.

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Transcription profiling of Arabidopsis roots after Iron deficiency

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