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Bulk RNA-sequencing of hypocotyl explant-derived calli of Arabidopsis WT and rap2.12-2

ABSTRACT: Plants are aerobic organisms that rely on molecular oxygen for respiratory energy production. Hypoxic conditions, with oxygen levels ranging between 1% and 5%, usually limit aerobic respiration and affect plant growth and development. Here, we demonstrate that hypoxic microenvironment induced by active cell proliferation during the two-step plant regeneration process intrinsically represses the regeneration competence of callus in Arabidopsis thaliana. Hypoxia-repressed plant regeneration was mediated by the RELATED TO APETALA 2.12 (RAP2.12) protein, a member of the Ethylene Response Factor VII (ERF-VII) family. The hypoxia-activated RAP2.12 protein promoted salicylic acid (SA) biosynthesis and defense responses, inhibiting pluripotency acquisition and de novo shoot regeneration in calli. RAP2.12 could bind directly to the SALICYLIC ACID INDUCTION DEFICIENT 2 (SID2) gene promoter and activate SA biosynthesis, repressing plant regeneration via a PLETHORA (PLT)-dependent pathway. The rap2.12 mutant calli exhibited enhanced shoot regeneration, which was impaired by SA treatment. Taken together, our findings demonstrate that cell proliferation-dependent hypoxic microenvironment reduces cellular pluripotency and plant regeneration through the RAP2.12–SID2 module.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE249447 | GEO | 2024/02/16

REPOSITORIES: GEO

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Bulk RNA-sequencing of hypocotyl explants and hypocotyl explant-derived calli of Arabidopsis

Project description:Plants are aerobic organisms that rely on molecular oxygen for respiratory energy production. Hypoxic conditions, with oxygen levels ranging between 1% and 5%, usually limit aerobic respiration and affect plant growth and development. Here, we demonstrate that hypoxic microenvironment induced by active cell proliferation during the two-step plant regeneration process intrinsically represses the regeneration competence of callus in Arabidopsis thaliana. Hypoxia-repressed plant regeneration was mediated by the RELATED TO APETALA 2.12 (RAP2.12) protein, a member of the Ethylene Response Factor VII (ERF-VII) family. The hypoxia-activated RAP2.12 protein promoted salicylic acid (SA) biosynthesis and defense responses, inhibiting pluripotency acquisition and de novo shoot regeneration in calli. RAP2.12 could bind directly to the SALICYLIC ACID INDUCTION DEFICIENT 2 (SID2) gene promoter and activate SA biosynthesis, repressing plant regeneration via a PLETHORA (PLT)-dependent pathway. The rap2.12 mutant calli exhibited enhanced shoot regeneration, which was impaired by SA treatment. Taken together, our findings demonstrate that cell proliferation-dependent hypoxic microenvironment reduces cellular pluripotency and plant regeneration through the RAP2.12–SID2 module.

2024-02-16 | GSE249446 | GEO

Thioredoxin DCC1 regulates shoot regeneration through modulating multiple genes expression by RNA-seq analyses in Arabidopsis

Project description:The capacity of plant regeneration in different ecotypes of Arabidopsis largely varies. However, the mechanism underlying this process remains exclusive. Here, we identified a critical thioredoxin gene DCC1 in determining natural variation for shoot regeneration in Arabidopsis. Functional loss of DCC1 resulted in the repression of shoot regeneration. DCC1 encodes a thioredoxin, which was localized in mitochondria. DCC1 directly interacted with CARBONIC ANHYDRASE 2 (CA2) to regulate the mitochondrial respiratory complex activity and mediate the Reactive Oxygen Species (ROS) level. Defects of DCC1 or CA2 caused the increased ROS level. To understand the regulatory mechanism of DCC1-mediated ROS in shoot regeneration, we analyzed the transcript levels of wild type Col-0 and the mutant dcc1 calli during shoot regeneration by RNA-seq. Three biological repeats of wild type Co-0 and the mutant dcc1 calli were used for RNA sequencing. Total RNAs were isolated from the calli of wild type Col-0 and the mutant dcc1 cultured on shoot-induction medium. The RNA-seq was performed using the Illumina Hiseq 2500. The raw reads were aligned to the genome sequences of TAIR10 using Tophat2 software. The gene expression levels were measured in FPKM, and many critical genes were identified to be involved in shoot regeneration.

2018-05-06 | E-MTAB-5236 | biostudies-arrayexpress

Regulation of the microsomal proteome by salicylic acid and deficiency of phosphatidylinositol‐4‐kinases β1 and β2 in Arabidopsis thaliana

Project description:Phosphatidylinositol-4-kinases β1 and β2 (PI4Kβ1/PI4Kβ2), which are responsible for phosphorylation of phosphoinositol to phosphatidylinositol-4-phosphate, have an important role in vesicular trafficking in plants. Moreover, PI4Kβ1/PI4β2 negatively regulate biosynthesis of phytohormone salicylic acid (SA). SA plays crucial role in plant immune responses and its endogenous concentration strongly affects plant transcriptome. In this study we were focused on the effect of the PI4Kβ1/PI4Kβ2 and SA on the abundance of membrane proteins. For this purpose, we performed proteomic analysis on isolated microsomal fractions from leaves of four Arabidopsis thaliana genotypes: wild type ecotype Columbia-0; double mutant impaired in function of PI4Kβ1/PI4Kβ2 (pi4kβ1/pi4kβ2) exhibiting high SA level; sid2 mutant with impaired SA biosynthesis depending on the isochorismate synthase 1 and triple mutant sid2/pi4kβ1/pi4kβ2. In total, we identified 4534 proteins from which 1696 proteins differed in abundance between the mutants and WT. We showed that SA has a big impact on membrane proteome, because among hundreds of the identified affected proteins typical proteins associated with SA triggered pathway occurred. Our data thus point out new connections between SA pathway and clathrin independent endocytosis (flotillins) and exocytosis/protein secretion (syntaxins, tertraspanin) to be investigated in future. In contrast to SA, presence/absence of PI4Kβ1/PI4Kβ2 itself affected only 27 proteins. Nevertheless, among them we identified CERK1, plasma membrane receptor for chitin. Although PI4Kβ1/PI4Kβ2 itself did not have strong impact on A. thaliana microsomal proteome, our data clearly shows that PI4Kβ1/PI4Kβ2 enhance the proteome changes when SA pathway is modulated in parallel

2021-02-24 | PXD019737 | Pride

Expression data from WT, sid2-1

Project description:Salicylic acid (SA) levels increase in Arabidopsis upon exposure to low temperature for more than a week. This cold-induced SA biosynthesis was found to proceed through the isochorismate synthase (ICS) pathway. The sid2-1 mutant is deficient in ICS1 and does not make SA at low temperature. We used microarray analysis to examine the genes differentially regulated by low temperature that were dependent on SA

2013-06-30 | GSE43819 | GEO

Expression data from WT, sid2-1

2013-06-30 | E-GEOD-43819 | biostudies-arrayexpress

AtPRMT5 regulates shoot regeneration through modulating multiple genes expression analyzed by RNA-seq

Project description:Protein arginine methylation plays essential roles in diverse biological processes, but its role in regulating shoot regeneration remains elusive. In this study, we analyzed the function of the protein arginine methyltransferase AtPRMT5 during de novo shoot regeneration in Arabidopsis. AtPRMT5 encodes a type II PRMT that methylates proteins, including histones and RNA splicing factors. Mutation of AtPMRT5 decreased the frequency of shoot regeneration and number of shoots per callus in the atprmt5 mutant compared with those of the wild type. To understand the mechanism of AtPRMT5 regulation of shoot regeneration, we analyzed the transcript levels of wild type and the mutant atprmt5 calli during shoot regeneration by RNA-seq. Three biological repeats of wild type and the mutant atprmt5-1 calli were used for RNA sequencing. Total RNAs were isolated from the calli of wild type Col and the mutant atprmt5-1 cultured on cultured on shoot-induction medium. The RNA-seq llibraries were constructed with TruSeq Stranded mRNA Library Prep Kit and sequenced using the Illumina Hiseq 2500. The raw reads were aligned to the genome sequences of TAIR10 using Tophat software. The gene expression levels were measured in RPKM, and many critical genes regulated by AtPRMT5 were identified to be involved in shoot regeneration.

2017-06-18 | E-MTAB-5044 | biostudies-arrayexpress

Hypoxic gene expression in med25-1

Project description:Plants as obligate aerobic organisms are severely affected by flooding-induced oxygen restriction. As a consequence, they suffer from energy deficits which are counterbalanced by activation of anaerobic metabolism genes through subgroup VII ETHYLENE-RESPONSE FACTOR (ERFVII) transcription factors. Despite the crucial role of ERFVIIs in regulating transcript responses to hypoxia in multiple plant species, it is not understood how these factors mechanistically initiate hypoxic gene expression. Here, we show that the Arabidopsis ERFVIIs RELATED TO APETALA 2.12 (RAP2.12) and RAP2.2 recruit the Mediator complex, present in all higher eukaryotes, in order to convey stress signals to RNA polymerase II. This is achieved by specific interaction with Mediator subunit 25 (AtMED25). Both RAP2.12 and RAP2.2 require AtMED25 for full activity and subsequent induction of target hypoxia core genes. Our findings support an interplay of multiple coactivators under hypoxia and underline the flexible nature of the Mediator complex composition, which both help to meet specific cellular demands under (hypoxic) stress conditions.

2019-12-31 | GSE130962 | GEO

Expression analysis of Arabidopsis plants infected with Pseudomonas syringae pv. tomato DC3000 (Pto) strains

Project description:Effector-Triggered Immunity (ETI) and Pattern-Triggered Immunity (PTI) are well-defined modes of plant immunity triggered by recognition of pathogen effector proteins and microbe-associated molecular patterns, respectively. While ETI and PTI network extensively share signaling components, the shared components are used in different ways, resulting in distinct network properties in the model plant Arabidopsis: immunity is highly robust against network perturbations in ETI but relatively sensitive in PTI. However, the molecular mechanism how the shared network leads to the different properties is not known. Here we show that salicylic acid (SA) reponsive genes can respond in the absense of SA during ETI. A 24 DNA microarray study using total RNA from Arabidopsis wildtype Col-0 and sid2-2 mutant infected with Pto hrcC-, Pto EV, Pto AvrRpt2 or water.

2014-07-29 | E-GEOD-40544 | biostudies-arrayexpress

A Tripartite Amplification Loop Involving WRKY75, Salicylic Acid and ROS Accelerates Leaf Senescence in Arabidopsis

Project description:Leaf senescence is a highly coordinated and complicated process with the integration of numerous internal and environmental signals. Salicylic acid (SA) and reactive oxygen species (ROS) are two well-defined inducers of leaf senescence, whose contents progressively and inter-dependently increase during leaf senescence via a yet unknown mechanism. Here, we have characterized a newly identified positive regulator of leaf senescence, WRKY75, and demonstrated that knock-down or knock-out of WRKY75 delays, while over-expression of WRKY75 accelerates age-dependent leaf senescence. The WRKY75 transcription is induced by age, SA, H2O2, as well as multiple plant hormones. Meanwhile, WRKY75 is able to promote SA production by inducing the transcription of SA INDUCTION-DEFICIENT 2 (SID2), and suppress H2O2 scavenging partly by repressing the transcription of CATALASE 2 (CAT2). Genetic analysis reveals that the SID2 mutation or an increase of catalase activity rescues the precocious leaf senescence phenotype evoked by WRKY75 over-expression. Based on these results, we propose a “tripartite amplification loop” model in which WRKY75, SA and ROS undergo a gradual but self-sustained rise driven by three interlinked positive feedback regulations. This tripartite amplification loop provides a molecular framework connecting the upstream signals, such as age, ethylene, JA and ABA, to the downstream regulatory network executed by those SA-responsive and H2O2-responsive transcription factors during leaf senescence.

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Expression analysis of Arabidopsis transgenic plants carrying DEX-inducible MKK4DD in Col or sid2 background treated with DEX or control

Project description:Effector-Triggered Immunity (ETI) and Pattern-Triggered Immunity (PTI) are well-defined modes of plant immunity triggered by recognition of pathogen effector proteins and microbe-associated molecular patterns, respectively. While ETI and PTI network extensively share signaling components, the shared components are used in different ways, resulting in distinct network properties in the model plant Arabidopsis: immunity is highly robust against network perturbations in ETI but relatively sensitive in PTI. However, the molecular mechanism how the shared network leads to the different properties is not known. Here we show that sustained MAPK activation compensate salicylic acid (SA) signaling. A 12 DNA microarray study using total RNA from Arabidopsis transgenic plants carrying DEX-inducible MKK4DD in Col or sid2-2 background treated with DEX or control.

2014-07-29 | E-GEOD-40547 | biostudies-arrayexpress

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