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Transcript profile changes associated with lateral root fasciation in temperature-sensitive mutants

ABSTRACT: Control of the dimensions of organ primordia is crucial for proper organogenesis in the development of multicellular organisms. Lateral root formation is a major type of plant organogenesis important for postembryonic development of the root system. Lateral root formation begins with a few rounds of asymmetric, anticlinal cell division (formative cell division) in the pericycle, which determines the basal dimensions of root primordia. Here we show, based on molecular genetic analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis thaliana, that mitochondria play an unexpected role in the restriction of formative cell division and thus in the control of the basal dimensions of lateral root primordia. Three TDF mutants, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), exhibit lateral root fasciation from excess formative cell division under high-temperature conditions. We identify RRD1 as encoding a poly(A)-specific ribonuclease (PARN)-like protein and RRD2 and RID4 as encoding pentatricopeptide repeat (PPR) proteins. Subcellular localization and predicted functions of these proteins implicate them in poly(A)-dependent RNA degradation in mitochondria. This characterization is supported by the finding that mitochondrial RNAs with poly(A) tails, most of which are mRNAs of respiratory chain components, accumulate at an unusually high level in these TDF mutants.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE34595 | GEO | 2012/02/10

SECONDARY ACCESSION(S): PRJNA150487

REPOSITORIES: GEO

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Transcript profile changes associated with lateral root fasciation in temperature-sensitive mutants

Project description:Control of the dimensions of organ primordia is crucial for proper organogenesis in the development of multicellular organisms. Lateral root formation is a major type of plant organogenesis important for postembryonic development of the root system. Lateral root formation begins with a few rounds of asymmetric, anticlinal cell division (formative cell division) in the pericycle, which determines the basal dimensions of root primordia. Here we show, based on molecular genetic analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis thaliana, that mitochondria play an unexpected role in the restriction of formative cell division and thus in the control of the basal dimensions of lateral root primordia. Three TDF mutants, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), exhibit lateral root fasciation from excess formative cell division under high-temperature conditions. We identify RRD1 as encoding a poly(A)-specific ribonuclease (PARN)-like protein and RRD2 and RID4 as encoding pentatricopeptide repeat (PPR) proteins. Subcellular localization and predicted functions of these proteins implicate them in poly(A)-dependent RNA degradation in mitochondria. This characterization is supported by the finding that mitochondrial RNAs with poly(A) tails, most of which are mRNAs of respiratory chain components, accumulate at an unusually high level in these TDF mutants. Explants of three mutants (rrd1, rrd2, rid4) and wild type were cultured on B5 medium supplemented with 0.5 mg/L IBA for the induction of lateral root formation. After 12 hours of culture at 28C, explants were collected and used for microarray analysis. Analysis was performed in three biological replicates.

2012-02-10 | E-GEOD-34595 | biostudies-arrayexpress

A YTHDF-PABP axis is required for m6A-mediated organogenesis in plants

Project description:N6-methyladenosine (m6A) in mRNA is key to eukaryotic gene regulation. Many m6A functions involve RNA-binding proteins that recognize m6A via a YT521-B Homology (YTH) domain. YTH domain proteins contain long intrinsically disordered regions (IDRs) that may mediate phase separation and interaction with protein partners, but whose precise biochemical functions remain largely unknown. The Arabidopsis thaliana YTH domain proteins ECT2, ECT3 and ECT4 accelerate organogenesis through stimulation of cell division in organ primordia. Here, we use ECT2 to reveal molecular underpinnings of this function. We show that stimulation of leaf formation requires the long N-terminal IDR, and we identify two short IDR-elements required for ECT2-mediated organogenesis. Of these two, a 19-amino acid region containing a tyrosine-rich motif conserved in both plant and metazoan YTHDF proteins is necessary for binding to the major cytoplasmic poly(A)-binding proteins PAB2, PAB4 and PAB8. Remarkably, overexpression of PAB4 in leaf primordia partially rescues the delayed leaf formation in ect2 ect3 ect4 mutants, suggesting that the ECT2-PAB2/4/8 interaction on target mRNAs of organogenesis-related genes may overcome limiting PAB concentrations in primordial cells.

2023-11-28 | PXD045801 | Pride

Profiling downstream targets of PUCHI in roots of Arabidopsis thaliana

Project description:Lateral root organogenesis plays an essential role in defining plant root system architecture. In Arabidopsis, the AP2-family transcription factor PUCHI controls cell proliferation in lateral root primordia. To identify downstream targets of PUCHI, we engineered a transgenic line with inducible PUCHI activity by expressing a fusion protein of PUCHI and rat glucocorticoid receptor (GR) under the control of its own regulatory region (gPUCHI-GR) in the puchi-1 mutant.

2019-06-12 | GSE128721 | GEO

The Arabidopsis TETRATRICOPEPTIDE-REPEAT THIOREDOXIN-LIKE (TTL) family members are involved in root system formation via their interaction with cytoskeleton and cell wall remodeling

Project description:Lateral roots are essential components of the plant edaphic interface; contributing to water and nutrient uptake, biotic and abiotic interactions, stress survival, and plant anchorage. We have identified the TETRATRICOPEPTIDE-REPEAT THIOREDOXIN-LIKE 3 (TTL3) gene as being related to lateral root emergence and later development. Loss of function of TTL3 leads to a reduced number of emerged lateral roots due to delayed development of lateral root primordia. This trait is further enhanced in the triple mutant ttl1ttl3ttl4. TTL3 interacts with microtubules and endomembranes and is known to participate in the brassinosteroid signaling pathway. Both ttl3 and ttl1ttl3ttl4 mutants are less sensitive to brassinosteroid treatment in terms of lateral root formation and primary root growth. The ability of TTL3 to modulate biophysical properties of the cell wall was established under restrictive conditions of hyperosmotic stress and loss of root growth recovery, which was enhanced in ttl1ttl3ttl4. Timing and spatial distribution of TTL3 expression is consistent with its role in development of lateral root primordia before their emergence and subsequent growth of lateral roots. TTL3 emerged as a novel component of the root system morphogenesis regulatory network.

2023-07-26 | PXD036355 | Pride

Identification of auxin and cytokinin cross-talk components involved in lateral root initiation

Project description:Genome wide transcriptome profiling of pericycle cells from roots exposed to auxin, cytokinin and both hormones simultaneously. Lateral root organogenesis in Arabidopsis is governed by a complex network of hormonal regulations. Plant hormones auxin and cytokinin were demonstrated to be the key regulators of this lateral root organogenesis and their mode of interaction is antagonistic. The aim of the project is to understand the role of the auxin - cytokinin signalling pathways in lateral root organogenesis.

2020-03-13 | GSE146778 | GEO

A single cell view of the transcriptome during lateral root initiation

Project description:Plant root architecture is a major determinant of fitness, and is under constant modification in response to favorable and unfavorable environmental stimuli. Beyond impacts on the primary root, the environment can also alter the position, spacing, density, and length of secondary or lateral roots. Lateral root development is among the best-studied developmental processes in Arabidopsis thaliana, yet the earliest steps of organogenesis remain elusive. Among the challenges faced in capturing these early molecular events is the fact that this process occurs in a small number of cells with unpredictable timing. The advent of single-cell sequencing affords the opportunity to isolate cells undergoing this fate transition and examine their transcriptomes independently. Using this approach, we successfully captured the transcriptomes of lateral root primordia and discovered many previously unreported upregulated genes. To further study this process, we developed a method to selectively repress genes in the xylem pole pericycle cells where lateral roots originate. We found that expression of several of the upregulated genes was required for normal root development. In addition, we discovered a subpopulation of cells in the endodermal cell file that respond to lateral root initiation, further highlighting the benefits of the single cell approach.

2021-01-01 | GSE158761 | GEO

CPL4 is a suppressor of de novo shoot organogenesis from roots of Arabidopsis thaliana

Project description:De novo shoot organogenesis (DNSO) is a commonly used pathway for plant biotechnology, and is a hormonally regulated process, where auxin and cytokinin coordinates suites of genes encoding transcription factors, general transcription factors, and RNA metabolism machinery genes. Here we report that silencing Arabidopsis thaliana CTD phosphatase-like 4 (CPL4RNAi), which increases phosphorylation level of RNA polymerase II (pol II) CTD, altered lateral root development and DNSO efficiency of the host plants, suggesting an importance of precise control of pol II activities during DNSO. Under standard condition, roots of CPL4RNAi lines produced no or few lateral roots. When induced by high concentration of auxin, CPL4RNAi lines failed to produce focused auxin maxima at the meristem of lateral root primordia, and produced fasciated lateral roots. By contrast, root explants of CPL4RNAi lines were highly competent for DNSO. Efficient DNSO of CPL4RNAi lines were observed even under 10 times less cytokinin required for wild type explants. Transcriptome analysis showed CPL4RNAi but not wild type explants expressed high levels of shoot meristem related genes during priming by high auxin/cytokinin ratio, and subsequent shoot induction with cytokinin. These results indicate that CPL4 functions as a repressor of the early stage of DNSO, during acquisition of competency by high auxin/cytokinin ratio, perhaps via regulation of pol II activities.

2020-09-19 | GSE104083 | GEO

Adventitious root formation in Populus trichocarpa involves complex cellular events

Project description:Stem cuttings of P. trichocarpa (clone 101-74) were rooted in liquid medium without growth regulators (basal medium). The first emerging roots were observed on cuttings 6 days after the start of culture. The highest average root number per cutting (10 ± 2 roots/cutting) was obtained after 14 days. The first macroscopic evidence of root initiation was the appearance of root primordia, as lateral bulges observed at the stem surface 3 to 4 days after transfer to basal medium. Stem cross-sections showed intensely dividing cells forming root primordial. One to two days later the bark split and the organized sequence of cell division and differentiation steps in the primordium led to the establishment of the main root tissues, as well as the vascular connections of the incipient root with the pre-existing stem vasculature. Subsequently, the outgrowth and emergence of the adventitious root occurred. We refer to the dormant cutting as stage 0, the organizing primordium as stage 1, the primordium differentiation as stage 2. To examine changes in gene transcription associated with the development of adventitious roots, we monitored the transcript levels in differentiating primordia using microarrays. cDNA was prepared from replicate sets of P. trichocarpa rooted cuttings harvested at stages 0, 1 and 2.

2012-11-01 | GSE34096 | GEO

Rice Lateral Root Inducible System timeseries

Project description:To transcriptionally characterize lateral root development in rice, we subjected the rice LRIS to genome-wide transcript profiling via RNA-sequencing. Taking into account the appearance of the first (stage I primordium) cell divisions starting from 6 hours after NAA treatment, we sampled at 2 hours and at 5 hours after NAA treatment to capture the primary auxin response and the gene expression related to initiation, respectively. Additionally, we sampled at 8 hours, 14 hours and 20 hours, in which the root was highly enriched for stage I, II and III primordia, respectively. As the spatiotemporal assessment of the primordia in the LRIS showed a highly synchronous induction and development of lateral roots in particular in the region just above the root meristem, root sections between 750 µm and 2000 µm from the root tip were microdissected and used for RNA-extraction. To assess possible artefacts induced by the replacement of the medium, we sampled a control before and 2 hours after replacement with NPA containing medium.

2023-08-24 | E-MTAB-13094 | biostudies-arrayexpress

Time-series RNAseq analysis following lateral root induction by gravistimulation

Project description:We report the comparison of transcriptomic profiles in specific lateral root tissues for Col-0 wild type and puchi-1 mutant seedlings. Lateral root organogenesis is a key process in plant root system development and adaptation to the environment. To dissect the molecular events occurring during the early phase, we generated time-series transcriptomic datasets profiling lateral root development in puchi-1 and wild type backgrounds. Consistent with a mutually inhibitory mechanism, transcriptomic and reporter analysis revealed meristem-related genes were ectopically expressed during early stages of lateral root primordium formation in puchi-1. We conclude that PUCHI participates to the coordination of lateral root patterning and represses ectopic establishment of meristematic cell identities during early stages of organ development.

2022-03-25 | GSE199142 | GEO

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