Transcriptome comparison of tobacco cell cultures to address mechanism of auxin autonomous cell proliferation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1153984 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The response to auxin is regulated by spatiotemporally specific expression of the auxin signalling machinery and by precise regulation of auxin concentration through multiple biosynthetic and metabolite pathways supported by auxin transport involving influx, efflux, and intracellular transport. The rapid and steady proliferation of cells in plant cell cultures presents unique model for studying mechanisms involved in cell cycle regulation. Here we present transcriptome analyses in the habituated auxin-autonomous BY-2H and VBI-2 cell lines.
2024-12-31 | GSE275968 | GEO
Project description:Wild tobacco flowers wave rhythmically to facilitate specific pollinator interactions. This movement behavior is controlled by a regulatory network that involves the circadian clock- and auxin-signaling pathways. The plant hormone auxin, similarly to its function in tropic movements, acts as growth regulator in the circadian regulation of floral movement. Dorsoventral asymmetry in auxin levels and auxin transcriptional responses mediate the growth responses in the floral peduncle that make flowers move. Multiple components of the auxin-signaling pathway and auxin responses are under the control of circadian clock. However, it is unclear where these two pathways intersect and how collectively contribute to regulate specific rhythmic outputs. Here we found that the blue light photoreceptor and circadian clock component ZEITLUPE (ZTL) controls auxin responses through the regulation of the auxin-signaling pathway in a time-of-day and blue light specific manner. Abrogation of ZTL expression abolishes flower movement and the temporal gating of auxin-induced growth responses in the floral peduncle. ZTL regulates transcription and directly interacts with indole-3-acetic acid inducible 19 (IAA19), a circadian controlled gene that regulates development of curvature in moving organs. Indicating that ZTL modulates auxin sensitivity in part through the regulation of AUX/IAA transcriptional repressors. At night, growth responses in the peduncle to the synthetic auxin 2,4-D revealed that ZTL additionally controls auxin responses regulating auxin homeostasis. These results indicate that ZTL conveys temporal and environmental information, at multiple levels, into the auxin signaling-pathway and in this way sculpts the temporal gating of auxin responses that allow flowers to move. To gain further insight into the molecular basis of the movement of flowers we used a whole genome microarray as a discovery platform to identify genes differentially expressed in adaxial and abaxial sides of the floral peduncle at different stages of the movement.
2020-01-31 | GSE117235 | GEO
Project description:Wild tobacco flowers wave rhythmically to facilitate specific pollinator interactions. This movement behavior is controlled by a regulatory network that involves the circadian clock- and auxin-signaling pathways. The plant hormone auxin, similarly to its function in tropic movements, acts as growth regulator in the circadian regulation of floral movement. Dorsoventral asymmetry in auxin levels and auxin transcriptional responses mediate the growth responses in the floral peduncle that make flowers move. Multiple components of the auxin-signaling pathway and auxin responses are under the control of circadian clock. However, it is unclear where these two pathways intersect and how collectively contribute to regulate specific rhythmic outputs. Here we found that the blue light photoreceptor and circadian clock component ZEITLUPE (ZTL) controls auxin responses through the regulation of the auxin-signaling pathway in a time-of-day and blue light specific manner. Abrogation of ZTL expression abolishes flower movement and the temporal gating of auxin-induced growth responses in the floral peduncle. ZTL regulates transcription and directly interacts with indole-3-acetic acid inducible 19 (IAA19), a circadian controlled gene that regulates development of curvature in moving organs. Indicating that ZTL modulates auxin sensitivity in part through the regulation of AUX/IAA transcriptional repressors. At night, growth responses in the peduncle to the synthetic auxin 2,4-D revealed that ZTL additionally controls auxin responses regulating auxin homeostasis. These results indicate that ZTL conveys temporal and environmental information, at multiple levels, into the auxin signaling-pathway and in this way sculpts the temporal gating of auxin responses that allow flowers to move. To gain further insight into the molecular basis of temporal regulation of the movement of flowers we used a whole genome microarray as a discovery platform to identify genes differentially expressed in a RNAi knockdown line silenced in the expression of the circadian clock component ZEITLUPE (irZTL-314).
2019-06-30 | GSE116648 | GEO
Project description:RNA-seq of tobacco explants cultured by different NAA concentrations during in vitro tissue culture provides high-resolution transcriptome data,which provides a novel direction and theoretical basis for improving gene editing efficiency in plants by modulating chromatin accessibility through auxin signaling and tissue culture conditions.
2024-12-01 | GSE280743 | GEO
Project description:The phytohormone auxin controls a myriad of processes in plants, at least in part through its regulation of cell expansion. The "acid growth hypothesis" has been proposed to explain auxin-stimulated cell expansion for five decades, but the mechanism underlying auxin-induced cell wall acidification is poorly characterized. Auxin induces the phosphorylation and activation of the plasma membrane (PM) H+-ATPase that pumps protons into the apoplast, yet how auxin activates its phosphorylation remains elusive. Here, we show that the transmembrane kinase (TMK) auxin signaling proteins interact with PM H+-ATPases and activate their phosphorylation to promote cell wall acidification and hypocotyl cell elongation in Arabidopsis. Auxin induced TMK's interaction with H+-ATPase on the plasma membrane within 1-2 minutes as well as TMK-dependent phosphorylation of the penultimate Thr residue. Genetic, biochemical, and molecular evidence demonstrates that TMKs directly phosphorylate PM H+-ATPase and are required for auxin-induced PM H+-ATPase activation, apoplastic acidification, and cell expansion. Thus, our findings reveal a crucial connection between auxin and PM H+-ATPase activation in regulating apoplastic pH changes and cell expansion via TMK-based cell surface auxin signaling.
2021-07-14 | MSV000087822 | MassIVE
Project description:Auxin plays diverse and profound roles in plants, regulating essentially all aspects of plant growth and development. Yet how auxin achieves such functional diversity and specificity is largely unknown. Here, we address how different concentrations of auxin determine developmental responses through auxin signaling pathways, which are essential for differential growth including apical hook development. We showed that a high auxin concentration at concave side of the apical hook stimulated the C-terminus cleavage and cytosolic translocation of Transmembrane Kinase 1 (TMK1), which then phosphorylates non-canonical IAA32 and IAA34. Surprisingly, and in contrast to the previous report that auxin degrades IAA proteins through the TIR1/AFB auxin receptor to regulate gene expression, here we found that non-canonical IAA32 and IAA34 proteins were stabilized by the high auxin concentration through TMK1 cleavage to negatively regulate gene expression and inhibit growth. Thus, we demonstrated that TIR1/AFB-independent transcriptional auxin signaling regulated growth inhibition in response to the high auxin concentration.
2019-02-12 | GSE111716 | GEO
Project description:Canonical auxin signalling starts with auxin binding to the receptor complex, followed by modulation of gene transcription and protein abundance (Tan et al., 2007; Chapman and Estelle, 2009; Slade et al., 2017). However, recent studies also showed an alternative mechanism in roots involving intra-cellular auxin perception, but not transcriptional reprogramming (Fendrych et al., 2018). Despite knowledge on effects of auxin on Arabidopsis root growth at the protein and phosphorylation level is increasing (Zhang et al., 2013; Mattei et al., 2013; Slade et al., 2017), it still remains incomplete. To address this gap in our knowledge, we explored the impact of auxin on the root tip proteome and phosphoproteome.
2021-09-09 | PXD021267 | Pride
Project description:Cell Autonomous and non-cell autonomous effects of neuronal Bin1 loss in vivo
| PRJNA558011 | ENA
Project description:The phytohormone auxin triggers transcriptional reprograming utilizing a well-characterized nuclear perception machinery. In contrast, mechanisms underlying other auxin effects, such as auxin feed-back on its transport, rapid regulation of ion fluxes or ultrafast global phospho-response, remain enigmatic. Auxin Binding Protein 1 (ABP1) has been contested as an auxin receptor candidate since decades. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at the acidic pH typical for the apoplast. ABP1 and its plasma membrane-localized partner, Transmembrane Kinase 1 (TMK1) are required for auxin-induced phosphorylation of about thousand proteins. Loss-of-function abp1 alleles but not complemented lines show defects in in vitro shoot regeneration and formation of auxin-transporting channels for vasculature formation and regeneration. These results support a role of ABP1-TMK1 in cell surface auxin perception mediating global auxin phospho-response and regenerative development.
2022-08-25 | PXD031063 | Pride
Project description:Proper functioning of the nuclear auxin pathway is essential for regulating plant growth and development by maintaining auxin homeostasis. To understand better physiological mechanisms involved in auxin signaling pathways we investigated the localization and effect of accumulation of auxin coreceptor IAA17/AXR3 in root. We demonstrate that the accumulation of stable nuclear AXR3-1 protein interferes with auxin homeostasis, causing auxin insensitivity and increased rapid root cell elongation followed by detained growth. This growth pattern is associated with changes in phytohormone gene expression. Data from transcriptomic screen combined with reporter lines and mutant studies declare essential role of auxin homeostasis in maintaining optimal root growth rate and development. We proposed a model in which rapid cell elongation is caused by combination of AXR3-1-dependent auxin insensitivity associated with unblocked gibberellin effect on root. This study demonstrate that plants coordinate gibberellin homeostasis by the auxin signaling pathway, contributing to avoid excessive root elongation.
2023-04-01 | GSE227820 | GEO