Transcriptome comparison of tobacco cell cultures to address mechanism of auxin autonomous cell proliferation
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ABSTRACT:
ORGANISM(S): Nicotiana tabacum
PROVIDER: GSE275968 | GEO | 2024/12/31
REPOSITORIES: GEO
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Project description:Transcriptome comparison of tobacco cell cultures to address mechanism of auxin autonomous cell proliferation
| PRJNA1153984 | ENA
Project description:Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in Setaria viridis and maize, we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, and glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A GFP-tagged construct of SvAUX1 under its native promoter showed that the AUX1 protein localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis finds that most gene expression modules are conserved between mutant and wildtype plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using CRISPR-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SvAUX1/SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, leaf, and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.
2022-01-13 | GSE193344 | GEO
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:Expression data after flg22 treatment on leaf discs in Col-0, 35S:AFB1 and 35S:miR393 We used microarrays to investigated the effect of auxin signalling on flg22 response pathway. We also compared if addition of auxin could simulated the 35S:AFB1 phenotype. Keywords: stress response, disease state analysis Leaf discs were taken and let overnight in water to avoid the wound response. We then performed the treatment (flg22, flg22 from Agrobacterium tumefaciens, flg22 +NAA, NAA) to the media. The samples where harvested and freeze in liquid nitrogen at 0, 1 and 2h after treatment.
2009-10-31 | E-GEOD-17479 | biostudies-arrayexpress
Project description:Publication title: Pseudonodule formation by wild type and symbiotic mutant Medicago truncatula in response to auxin transport inhibitors This SuperSeries is composed of the following subset Series: GSE27991: Expression data of Medicago truncatula Jemalong A17 roots treated with auxin transport inhibitors GSE28171: Expression data of Medicago truncatula Jemalong A17 roots treated with S. meliloti exoA mutant or auxin transport inhibitors GSE28172: Expression data of Medicago truncatula skl1-1 roots treated with S. meliloti wild-type or auxin transport inhibitors GSE28173: Genes differentially expressed in wild-type Medicago truncatula plants during nodulation Refer to individual Series
2011-03-25 | E-GEOD-28174 | biostudies-arrayexpress
Project description:The transport of auxin controls the rate, direction and localization of plant growth and development. The course of auxin transport is defined by the polar subcellular localization of the PIN proteins, a family of auxin efflux transporters. Using blue native PAGE and quantitative mass spectrometry, we identify native PIN core transport units as homo- and heteromers assembled from PIN1, 2, 3, 4 and 7 subunits only. To identify the protein composition of the larger, low stringency-solubilized PIN assembly we affinity-purified GFP-fused PIN proteins from Arabidopsis roots after expression from their native promoters and after the induction of discrete lateral roots, and analyzed the captured proteins by label-free quantitative mass spectrometry (LC-MS/MS).
2020-10-08 | PXD021543 | Pride
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:Lateral root initiation was used as a model system to study the mechanisms behind auxin-induced cell division. Genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the AUX/IAA signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation. Experiment Overall Design: Seedlings of both wild type (Col-0) and the lateral root defective mutant (slr-1) were germinated on MS medium supplemented with 10μM NPA (=auxin transport inhibitor). Three days after germination, such seedlings were transferred to MS supplemented with 10μM NAA for 0h, 2h and 6h respectively. The segment between root meristem and root-hypocotyl junction was harvested from about 1500 seedling per time point. All treatments were repeated biologically. 5.8 μg total RNA was used for the preparation of biotinylated cRNA. Labeled RNA was hybridised to ATH1 Affymetrix chips. The resulting data was MAS5.0 normalised.
2007-07-13 | E-GEOD-3350 | biostudies-arrayexpress
Project description:Auxin is essential for plant growth and development by altering downstream gene expression. Although large progresses have been made on auxin-concentration, distribution and signaling pathways in model plants like Arabidopsis and rice, little is known in moso bamboo which belongs to grass family, and has great economic and social value. Here we performed genome-wide analysis of the key components related to auxin action, and identified 13 YUCCA genes for auxin synthesis, 14 PIN-FORMED/PIN-like (PIN/PILS) proteins 7 AUXIN1/LIKE-AUX1 (AUX1/LAX) family members for auxin transport, 10 auxin binding factors (AFB) for auxin perception, 43 auxin/indole-3-aceticacid (AUX/IAA) and 41 auxin response transcription factors (ARF) genes for auxin signaling in moso bamboo genome. We further performed phylogenetic analysis of those auxin action related genes from Arabidopsis, Oryza sativa and moso bamboo. To know those genes’ ability to response exogenous auxin and to generate a comprehensive transcriptome overview of auxin response in moso Bamboo, we performed RNA_seq analysis. Our data showed that auxin regulates genes related its biosynthesis, transport, signaling. Moreover, we present the interaction between auxin and other phytohormones at the level of transcription. In summary, we identified the key gene families involved in the auxin action pathways in moso bamboo, and generated a transcriptional overview of the auxin response in moso bamboo. Our data open up an opportunity to uncover the precise roles of auxin action pathways in this important species.
2017-12-06 | GSE100172 | GEO
Project description:Following removal of its stem cell niche, the root meristem can regenerate by recruitment of remnant cells from the stump. Regeneration is initiated by rapid accumulation of auxin near the injury site but the source of this auxin is unknown. Here, we show that auxin accumulation arises from the activity of multiple auxin biosynthetic sources that are newly specified near the cut site and that their continuous activity is required for the regeneration process. Auxin synthesis is highly localized and PIN-mediate transport is dispensable for auxin accumulation and tip regeneration. Roots lacking the activity of the regeneration competence factor ERF115, or that are dissected at a zone of low-regeneration potential, fail to activate local auxin sources. Remarkably, restoring auxin supply is sufficient to confer regeneration capacity to these recalcitrant tissues. We suggest that regeneration competence relies on the ability to specify new local auxin sources in a precise spatio-temporal pattern.
2020-06-01 | GSE145488 | GEO