4f4a8e75bfa19a45d44a53e2cbcfc582 pmc_33513755.pdf c04372701b87d7e461e4989f0d3e4f38eb594a2b pmc_33513755.pdf f8c40fafc2e04a44f8d4eaffbd65de36af6bea14cd856412d0bce0de474689eb pmc_33513755.pdf Title: Transcriptomics Reveals Fast Changes in Salicylate and Jasmonate Signaling Pathways in Shoots of Carbonate-Tolerant Arabidopsis thaliana under Bicarbonate Exposure Subject: High bicarbonate concentrations of calcareous soils with high pH can affect crop performance due to different constraints. Among these, Fe deficiency has mostly been studied. The ability to mobilize sparingly soluble Fe is a key factor for tolerance. Here, a comparative transcriptomic analysis was performed with two naturally selected Arabidopsis thaliana demes, the carbonate-tolerant A1(c+) and the sensitive T6(c-). Analyses of plants exposed to either pH stress alone (pH 5.9 vs. pH 8.3) or to alkalinity caused by 10 mM NaHCO3 (pH 8.3) confirmed better growth and nutrient homeostasis of A1(c+) under alkaline conditions. RNA-sequencing (RNA-seq) revealed that bicarbonate quickly (3 h) induced Fe deficiency-related genes in T6(c-) leaves. Contrastingly, in A1(c+), initial changes concerned receptor-like proteins (RLP), jasmonate (JA) and salicylate (SA) pathways, methionine-derived glucosinolates (GS), sulfur starvation, starch degradation, and cell cycle. Our results suggest that leaves of carbonate-tolerant plants do not sense iron deficiency as fast as sensitive ones. This is in line with a more efficient Fe translocation to aerial parts. In A1(c+) leaves, the activation of other genes related to stress perception, signal transduction, GS, sulfur acquisition, and cell cycle precedes the induction of iron homeostasis mechanisms yielding an efficient response to bicarbonate stress. Keywords: transcriptomic; Arabidopsis thaliana; alkaline stress; glucosinolate; salicylate Author: Laura Pérez-Martín, Silvia Busoms, Roser Tolrà and Charlotte Poschenrieder Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Wed Jan 27 12:14:30 2021 CET ModDate: Wed Jan 27 12:25:00 2021 CET Custom Metadata: no Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 24 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 3988666 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- XYJQYJ+URWPalladioL-Ital Type 1 Custom yes yes no 10 0 HVFCKV+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 WSATAY+URWPalladioL-BoldItal Type 1 Custom yes yes no 19 0 SNYVBV+URWPalladioL-Roma Type 1 Custom yes yes no 23 0 IAFQNP+CMSY10 Type 1 Builtin yes yes no 27 0 GGHKEL+VnURWPalladioL-Bold Type 1 Custom yes yes 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2023-05-18) Date: 2024-10-02 03:33:17 CEST RepresentationInformation: pmc_33513755.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2023-03-31 12:08:43 CEST Size: 3988666 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 664 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: section.1 Item: Title: Results and Discussion Destination: section.2 Children: Item: Title: Fitness Characterization of A. thaliana Plants under High pH and Bicarbonate Stress Destination: subsection.2.1 Item: Title: Nutrient Content Profile Destination: subsection.2.2 Item: Title: Analysis of RNA-Seq Data Destination: subsection.2.3 Item: Title: Gene Ontology (GO) and Kioto Encyclopedia of Genes and Genomes (KEGG) Pathways under Bicarbonate Stress Destination: subsection.2.4 Item: Title: Signal Perception and Signal Transduction Destination: subsection.2.5 Children: Item: Title: Receptor-Like Kinases and Receptor-Like Proteins (RLK/RLP) Destination: subsubsection.2.5.1 Item: Title: Peroxidases Destination: subsubsection.2.5.2 Item: Title: Glutathione-Related Destination: subsubsection.2.5.3 Item: Title: Calmodulin Destination: subsubsection.2.5.4 Item: Title: Transcription Factors Destination: subsubsection.2.5.5 Item: Title: Protein Protein Interaction Network Functional Enrichment Analysis with Specific Bic-Induced Genes Destination: subsection.2.6 Item: Title: Mechanisms Underlying Differential bic Toxicity and Tolerance in A. thaliana Demes Destination: subsection.2.7 Item: Title: Materials and Methods Destination: section.3 Children: Item: Title: Plant Material Destination: subsection.3.1 Item: Title: Growth Conditions Destination: subsection.3.2 Item: Title: Physiological Trait Measurements Destination: subsection.3.3 Item: Title: RNA Isolation, Library Construction, and Sequencing Destination: subsection.3.4 Item: Title: Gene Ontology, KEGG Pathway, and Functional Protein Association Network Analysis of DEGs Destination: subsection.3.5 Item: Title: Relative Expression Analysis Destination: subsection.3.6 Item: Title: Statistical Analysis Destination: subsection.3.7 Item: Title: References Destination: subsection.3.7 Info: Title: Transcriptomics Reveals Fast Changes in Salicylate and Jasmonate Signaling Pathways in Shoots of Carbonate-Tolerant Arabidopsis thaliana under Bicarbonate Exposure Author: Laura Pérez-Martín, Silvia Busoms, Roser Tolrà and Charlotte Poschenrieder Subject: High bicarbonate concentrations of calcareous soils with high pH can affect crop performance due to different constraints. Among these, Fe deficiency has mostly been studied. The ability to mobilize sparingly soluble Fe is a key factor for tolerance. Here, a comparative transcriptomic analysis was performed with two naturally selected Arabidopsis thaliana demes, the carbonate-tolerant A1(c+) and the sensitive T6(c-). Analyses of plants exposed to either pH stress alone (pH 5.9 vs. pH 8.3) or to alkalinity caused by 10 mM NaHCO3 (pH 8.3) confirmed better growth and nutrient homeostasis of A1(c+) under alkaline conditions. RNA-sequencing (RNA-seq) revealed that bicarbonate quickly (3 h) induced Fe deficiency-related genes in T6(c-) leaves. Contrastingly, in A1(c+), initial changes concerned receptor-like proteins (RLP), jasmonate (JA) and salicylate (SA) pathways, methionine-derived glucosinolates (GS), sulfur starvation, starch degradation, and cell cycle. Our results suggest that leaves of carbonate-tolerant plants do not sense iron deficiency as fast as sensitive ones. This is in line with a more efficient Fe translocation to aerial parts. In A1(c+) leaves, the activation of other genes related to stress perception, signal transduction, GS, sulfur acquisition, and cell cycle precedes the induction of iron homeostasis mechanisms yielding an efficient response to bicarbonate stress. Keywords: transcriptomic; Arabidopsis thaliana; alkaline stress; glucosinolate; salicylate Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Wed Jan 27 12:14:30 CET 2021 ModDate: Wed Jan 27 12:25:00 CET 2021 ID: 0x078f5b3a911cff373121741663d7fb52, 0x078f5b3a911cff373121741663d7fb52 Filters: FilterPipeline: FlateDecode Fonts: Type1: Font: BaseFont: WSATAY+URWPalladioL-BoldItal FontSubset: true FirstChar: 65 LastChar: 116 FontDescriptor: FontName: WSATAY+URWPalladioL-BoldItal Flags: Symbolic FontBBox: -170, -300, 1073, 935 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: PNSTSZ+VnURWPalladioL FontSubset: true FirstChar: 129 LastChar: 226 FontDescriptor: FontName: PNSTSZ+VnURWPalladioL Flags: Symbolic FontBBox: -166, -283, 1021, 943 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: LEVXPH+EURM10 FontSubset: true FirstChar: 11 LastChar: 22 FontDescriptor: FontName: LEVXPH+EURM10 Flags: Symbolic FontBBox: -32, -243, 1060, 720 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