HSFA1 promotes cellular reprogramming in shoot regeneration III
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PROVIDER: PRJNA844588 | ENA |
REPOSITORIES: ENA
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Project description:HSFA1 promotes cellular reprogramming in shoot regeneration IV
| PRJNA971139 | ENA
Project description:Plants can regenerate from a variety of tissues on culturing in appropriate media. However, the metabolic shifts involved in callus formation and shoot regeneration are largely unknown. The metabolic profiles of callus generated from tomato (Solanum lycopersicum) cotyledons and that of shoot regenerated from callus were compared with the pct1-2 mutant that exhibits enhanced polar auxin transport and the shr mutant that exhibits elevated nitric oxide levels. The transformation from cotyledon to callus involved a major shift in metabolite profiles with denser metabolic networks in the callus. In contrast, the transformation from callus to shoot involved minor changes in the networks. The metabolic networks in pct1-2 and shr mutants were distinct from wild type and were rewired with shifts in endogenous hormones and metabolite interactions. The callus formation was accompanied by a reduction in the levels of metabolites involved in cell wall lignification and cellular immunity. On the contrary, the levels of monoamines were upregulated in the callus and regenerated shoot. The callus formation and shoot regeneration were accompanied by an increase in salicylic acid in wild type and mutants. The transformation to the callus and also to the shoot downregulated LST8 and upregulated TOR transcript levels indicating a putative linkage between metabolic shift and TOR signalling pathway. The network analysis indicates that shift in metabolite profiles during callus formation and shoot regeneration is governed by a complex interaction between metabolites and endogenous hormones.
2018-06-29 | MTBLS447 | MetaboLights
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
Project description:De novo shoot regeneration is an essential step for massive propagation and genetic engineering of elite germplasm in forestry. Poplar that is a fast growth tree species have a very important ecologically and economically role around the world, especially in China. In this study, we found that PtWOX11 that is a homologue of AtWOX11 not only involved de novo root formation but also promote de novo shoot regeneration in poplar. We demonstrated that PtWOX11 can enhance callus regeneration competence and shoot regeneration during two-step de novo shoot regeneration. Furthermore, by using RNA-seq and qPCR, we uncovered that during callus induction stage PtWOX11 activates PtPLTs expression to promote callus formation and regeneration competence, and promote PtCUC2/3, PtWUSa and PtSTM transcription to fulfil shoot organogenesis during shoot regeneration stage. Overall, our data indicated that PtWOX11 play a new function and transcriptional regulation mechanism on de novo shoot regeneration in poplar.
2018-03-26 | GSE101922 | GEO
Project description:Plants form callus and regenerate new organs when incubated on phytohormone-containing media. While accumulating evidence suggests that these regenerative processes are governed by transcriptional networks orchestrating stress responses and developmental transitions, it remains unknown if post-translational regulatory mechanisms are involved in this process. Here, we find that SIZ1, which encodes an E3 ligase catalyzing attachment of the SMALL UBIQUITIN-LIKE MODIFIER (SUMO) to proteins, regulates wound-induced signal transduction and organ regeneration. We show that loss-of-function mutants for SIZ1 exhibit over-production of shoot meristems under in vitro tissue culture conditions, while this defect is rescued in a complementation line expressing pSIZ1::SIZ1. RNA-sequencing analysis revealed that siz1-2 mutant exhibits enhanced transcriptional responses to wound stress, resulting in the hyper-induction of over 500 genes immediately after wounding. Among them, we show that elevated level of WOUND INDUCED DEDIFFERENTIATION 1 (WIND1) and WIND2 contribute to enhanced shoot regeneration observed in siz1 mutants, as the dominant-negative WIND1-SRDX partly rescues this phenotype in siz1-3. Although compromised SIZ1 function does not modify transcription of genes implicated in auxin-induced callus formation and/or pluripotency acquisition, it does lead to enhanced induction of cytokinin-induced shoot meristem regulators like WUSCHEL (WUS), promoting the formation of WUS-expressing foci in explants. This study thus suggests that SIZ1 negatively regulates shoot regeneration in part by repressing wound-induced cellular reprogramming.
2020-05-31 | GSE141188 | GEO
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
Project description:Injured plant somatic tissues regenerate themselves by establishing the shoot or root meristems. In Arabidopsis (Arabidopsis thaliana) a two-step culture system ensures regeneration by first promoting the acquisition of pluripotency and subsequently specifying the fate of new meristems. Although previous studies have reported the importance of phytohormones auxin and cytokinin in determining the fate of new meristems, it remains elusive whether and how the environmental factors influence this process. In this study, we investigated the impact of light signals on shoot regeneration using Arabidopsis hypocotyl as explants. We found that light signals promote shoot regeneration while inhibiting root formation. ELONGATED HYPOCOTYL 5 (HY5), the pivotal transcriptional factor in light signaling, plays a central role in this process by mediating the expression of key genes controlling the fate of new meristems. Specifically, HY5 directly represses root development genes and activates shoot meristem genes, leading to the establishment of shoot progenitor from pluripotent callus. We further demonstrated that the early activation of photosynthesis is critical for shoot initiation, and this is transcriptionally regulated downstream of the HY5-dependent pathways. In conclusion, we uncovered the intricate molecular mechanisms by which light signals control the establishment of new meristem through the regulatory network governed by HY5, thus, highlighting the influence of light signals on plant developmental plasticity.
2024-09-16 | GSE236147 | GEO
Project description:Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. We furthermore show that short exposures to the putative His kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of ahk and ahp mutants, as well as reporter lines for shoot markers and hormone responses suggests that TCSA at least partially works by impeding cytokinin signal transduction via AHK3, AHK4, AHP2, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins related to protein modification, transcriptional regulation, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, but also proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signalling (e.g., BIN2). Potentially novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM.
2022-09-28 | PXD030754 | Pride
Project description:Auxin and cytokinin can regulate callus formation from developed plant organs and shoot regeneration from callus. The regulation of dedifferentiation and regeneration of plant cells by auxin and cytokinin stimulation was considered to be caused by the regulation of reprograming of callus cells, but the hypothesis had been argued still in now. Although elucidation of the regulatory mechanisms of callus formation and shoot regeneration has helped advance plant biotechnology research, many plant species are intractable to transformation because of difficulties with callus regulation. In this study, we identified the compound Fipexide (FPX) as a useful regulatory compound through chemical biology-based screening. Compared with the activity of auxin and cytokinin, FPX showed higher efficiency as a chemical inducer in callus formation, shoot regeneration, and Agrobacterium infection. In regards to morphology, the cellular organization of FPX-induced callus differed from that produced under auxin/cytokinin conditions. According to a microarray analysis, the expressions of approximately 971 genes were two-fold up-regulated by FPX treatment for 2 days. Among these genes, 598 genes were also induced by auxin/cytokinin, while 373 genes, including metabolic regulation-related genes, were specifically expressed only under FPX treatment. FPX can promote callus formations in rice, poplar, and several vegetables. FPX should be a useful tool to reveal unknown mechanisms of plant development and to increase the number of transgenic plant species.
2018-07-12 | GSE116938 | GEO
Project description:Genomic reprogramming and cellular dedifferentiation are critical to the success of de novo tissue regeneration in lower vertebrates such as zebrafish and axolotl. ChIP-seq of the histone modifications H3K27Ac, H3K27me3, and H3K4me3 was used to characterize early epigenetic changes in a zebrafish in vivo model of adult muscle regeneration.
2019-12-06 | GSE137304 | GEO