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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Root development and responses are alerted by light

ABSTRACT: Investigation of whole genome gene expression level changes in Arabidopsis roots by the effect of light. Plant growth is sustained by a continuous cell division in meristems followed by cell differentiation and elongation. We have found that in Arabidopsis thaliana roots, flavonols play a key role in regulating the transition from cell division to differentiation. Using an engineered device to grow roots in darkness, but shoot in light cycle, coupled with transcriptomic and metabolomics analysis, we deciphered that flavonols accumulation regulates proliferation-promoting levels of auxin-PLETHORA and superoxide anion (O2-). High flavonols levels restrict auxin transport and the PLETHORA gradient but also superoxide radical content, promoting an accelerated cell differentiation. Furthermore, cytokinin-SHY2 and H2O2-UPB1 pathways, which promote differentiation and, respectively, antagonize auxin and O2- activity, increase flavonols biosynthesis establishing mutual interactions among these pathways. Flavonols function as positional signals integrating hormonal and ROS pathways to determine final organ growth. This work analyze the effect of root illumination in gene transcription. Details of how plants and roots are grown are described in Silva et al. (submitted) A six chip study using total RNA extracted from three independent experiments of Arabidopsis roots growing in presence of light and three independent experiments of Arabidopsis roots growing without light.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Juan del Pozo

PROVIDER: E-GEOD-68093 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Root development and responses are alerted by light

Project description:Investigation of whole genome gene expression level changes in Arabidopsis roots by the effect of light. Plant growth is sustained by a continuous cell division in meristems followed by cell differentiation and elongation. We have found that in Arabidopsis thaliana roots, flavonols play a key role in regulating the transition from cell division to differentiation. Using an engineered device to grow roots in darkness, but shoot in light cycle, coupled with transcriptomic and metabolomics analysis, we deciphered that flavonols accumulation regulates proliferation-promoting levels of auxin-PLETHORA and superoxide anion (O2-). High flavonols levels restrict auxin transport and the PLETHORA gradient but also superoxide radical content, promoting an accelerated cell differentiation. Furthermore, cytokinin-SHY2 and H2O2-UPB1 pathways, which promote differentiation and, respectively, antagonize auxin and O2- activity, increase flavonols biosynthesis establishing mutual interactions among these pathways. Flavonols function as positional signals integrating hormonal and ROS pathways to determine final organ growth. This work analyze the effect of root illumination in gene transcription. Details of how plants and roots are grown are described in Silva et al. (submitted)

2016-04-01 | GSE68093 | GEO

Spatiotemporal brassinosteroid signaling and antagonism with auxin control Arabidopsis root growth.

Project description:Analysis of brassinosteroid (BR) and auxin effects on gene expression in Arabidopsis roots. Our genomic results indicate that BR and auxin induce largely opposite gene expression responses in primary roots. RNA-Seq for 7-day-old Arabidopsis Col-0, dwf4, bri1-116, and bri1-116;bzr1-1D roots grown on regular medium and treated with brassinolide, auxin or mock solution for 4 hr.

2015-04-30 | E-GEOD-52966 | biostudies-arrayexpress

Auxin stimulates brassinosteroid biosynthesis in Arabidopsis roots

Project description:We found that auxin stimulates gene expression of DWF4, which encodes a rate-dertermining step in brassinosteroid biosynthesis pathways. This increased gene expressioin subsequently led to elevation of the biosynthetic flux in Arabidopsis roots. To determine the list of genes that are regulated by auxin-synthesizing brassinosteroids, we challenged Arabidopsis seedlings with either auxin only or auxin plus brassinosteroid biosynthetic inhibitor brassinazole. Keywords: Hormone treatment Arabidopsis seedlings (Columbia ecotype) were grown for 10 d on 1× MS agar-solidified media under long-day conditions (16:8, white light and dark cycle). The seedlings were then transferred to 2 different liquid media containing either 10–7 M 2,4-D or 10–7 M 2,4-D plus 10–6 M brassinazole. After 8 h of treatment, the seedlings were blotted with paper towels to remove excess media and subject to total RNA isolation. Total RNAs isolated from each batch were prepared from 3 replicate seedlings using an RNeasy plant mini kit (Qiagen, Germany).

2011-02-15 | E-GEOD-12964 | biostudies-arrayexpress

Auxin-triggered changes in the Arabidopsis root tip (phospho)proteome reveal novel root growth regulators

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

Cell type-specific auxin responses in the Arabidopsis thaliana root

Project description:We performed an analysis of transcriptomic responses to auxin within four distinct tissues of the Arabidopsis thaliana root. This high-resolution dataset shows how different cell types are predisposed to react to auxin with discrete transcriptional responses. The sensitivity provided by the analysis lies in the ability to detect cell-type specific responses diluted in organ-level analyses. This dataset provides a novel resource to examine how auxin, a widespread signal in plant development, influences differentiation and patterning in the plant through tissue-specific transcriptional regulation. To analyze the effect of auxin in separate spatial domains of the root, early transcriptional changes in response to auxin treatment were assayed by means of fluorescence activated cell sorting (FACS) and microarray analysis in four tissues of the Arabidopsis root (wild type Col-0). The samples covered inner and outer as well as proximal and distal cell populations; including the stele (reporter line pWOL::GFP), xylem-pole (xp) pericycle (enhancer trap line E3754), epidermis/lateral root cap (reporter line pWER::GFP) and columella (enhancer trap line PET111). One-week-old seedlings of the individual lines were treated with auxin (two hours, 5µM indole-3-acetic acid [IAA]) or mock treated, after which roots were harvested and cells were dissociated by cell wall digestion (1 hour; including 5uM IAA) . GFP-positive cells were sorted and used for microarray transcriptome analysis (as in Bargmann and Birnbaum, Plant Phys. 2010). For comparison, transcriptional responses to auxin were also assayed in intact (undigested) roots.

2013-08-06 | E-GEOD-35580 | biostudies-arrayexpress

Root nitrate response of wild type plants and afb3-1 mutant plants in Arabidopsis thaliana

Project description:Auxin is a key phytohormone regulating central processes in plants that include embryo development, lateral root growth and flower maturation among others. Auxin is sensed by a set of F-Box proteins of the TIR1/AFB3 family triggering auxin dependent responses by a pathway that involves an interplay between the Aux/IAA transcription repressors and the ARF transcription factors. We have previously shown that the AFB3 auxin receptor has a specific role in coordinating primary and lateral root growth to external and internal nitrate availability (Vidal et al., 2010). In this work, we used an integrated genomics, bioinformatics and molecular genetics approach to dissect regulatory networks acting downstream AFB3 that are activated by a transient nitrate treatment in Arabidopsis roots. Our systems approach unraveled key components of the AFB3 regulatory network leading to changes in lateral root growth in response to nitrate. Arabidopsis seedlings of the Ws and afb3-1 genotypes were grown on hydroponic medium containing 1X MS salts without Nitrogen, supplemented with 0.5 mM ammonium succinate as Nitrogen source and 3 mM sucrose on a Percival chamber under a photoperiod of 16 hours of light (100 Î¼E/m2/sec) and 8 hours of dark at 22Â°C for 14 days. The plants were treated at the onset of the light cycle with 5 mM KNO3 or 5 mM KCl as control for 2 hours. Whole roots were cut from seedlings and frozen on liquid Nitrogen. Total RNA was extracted using the TriZol reagent. 3 independent biological replicates were performed.

2012-04-30 | E-GEOD-35544 | biostudies-arrayexpress

Root isoprene formation alters lateral root development Maja Miloradovic van Doorn

Project description:Isoprene is a C5 volatile organic compound, which can protect aboveground plant tissue from abiotic stress such as short-term high temperatures and accumulation of reactive oxygen species (ROS). Here, we uncover new roles for isoprene in the plant belowground tissues. By analyzing Populus x canescens isoprene synthase (PcISPS) promoter reporter plants, we discovered PcISPS promoter activity in certain regions of the roots including the vascular tissue, the differentiation zone and the root cap. Treatment of roots with auxin or salt increased PcISPS promoter activity at these sites, especially in the developing lateral roots (LR). Transgenic, isoprene non-emitting poplar roots revealed an accumulation of O2 - in the same root regions where PcISPS promoter activity was localized. Absence of isoprene emission, moreover, increased the formation of LRs. Inhibition of NAD(P)H oxidase activity suppressed LR development, suggesting the involvement of ROS in this process. The analysis of the fine root proteome revealed a constitutive shift in the amount of several redox balance, signaling and development related proteins, such as superoxide dismutase, various peroxidases and linoleate 9S-lipoxygenase, in isoprene non-emitting poplar roots. Together our results indicate for isoprene a ROS-related function, eventually co-regulating the plant-internal signaling network and development processes in root tissue. This article is protected by copyright. All rights reserved.

2020-06-16 | PXD019789 | Pride

Transcription profiling of Arabidopsis - effect of AtHRE1 and AtHRE2 overexpression in normoxia and hypoxia

Project description:HRE1 and HRE2 are two ERF transcription factors induced by low oxygen. In this work we analyzed the effect of ectopic expression of HRE1 and HRE2 on the arabidopsis transcriptome in aerobic and hypoxic (1% O2) conditions. While HRE1 has a moderate effect on the expression of anaerobic genes under hypoxia, HRE2 does not affect them either under aerobic or hypoxic conditions. Experiment Overall Design: We treated Arabidopsis seedling Col-0 (wt) and transgenic 35S::HRE1 and 35S::HRE2 , 7-day old, germinated in 12/12 light/dark photoperiod with: Experiment Overall Design: -Control (23Â°C, dark, 21% O2, 4h). Experiment Overall Design: -Hypoxia (23Â°C, dark, 1% O2, 4h). Experiment Overall Design: Two biological replicates for each condition.

2009-11-10 | E-GEOD-17099 | biostudies-arrayexpress

Auxin signaling in the epidermis regulates stem growth via interactions with the brassinosteroid pathway

Project description:Growth of a complex multicellular organism requires coordinated changes in diverse cell types. These cellular changes generate organs of the correct size, shape and functionality. During plant development, the growth hormone auxin induces stem elongation; however, which cell types of the stem perceive the auxin signal and contribute to organ growth is poorly understood. Here, we show that auxin signalling is required in many cell types for correct hypocotyl stem growth, with a key role for the epidermis. Combining genetic manipulations in Arabidopsis thaliana with transcriptional profiling of the hypocotyl epidermis from Brassica rapa, we show that auxin functions in the epidermis in part by inducing activity of the locally-acting, growth-promoting brassinosteroid pathway. Our findings clarify cell-specific auxin function in the hypocotyl, and highlight the complexity of cell-type interactions within a growing organ. We performed whole-genome transcriptome (mRNA-Seq) on 5 d-old W light-grown Arabidopsis thaliana plants (CER6pro>>axr3-1::mCit experimental plants and UAS::axr3-1::mCit hemizygous control plants; whole-seedling tissue) treated for 4 h W light or low R:FR shade. In addition, we performed mRNA-Seq on 4 d-old Brassica rapa plants (FPsc strain) treated for 9 h W light or shade. Brassica tissues collected were hypocotyl epidermal peels or whole hypocotyls.

2016-06-30 | E-GEOD-79881 | biostudies-arrayexpress

Spatiotemporal brassinosteroid signaling and antagonism with auxin control Arabidopsis root growth.

2015-04-30 | GSE52966 | GEO

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