Ontology highlight
ABSTRACT:
PROVIDER: PRJNA610935 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11261930.fastq.gz | Fastqsanger.gz | |||
| SRR11261931.fastq.gz | Fastqsanger.gz | |||
| SRR11261932.fastq.gz | Fastqsanger.gz | |||
| SRR11261933.fastq.gz | Fastqsanger.gz | |||
| SRR11261934.fastq.gz | Fastqsanger.gz |
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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
Project description:TRH1, also classified as KUP4, belongs in the family of plant HAK/KUP/KT (High-Affinity K+/ K+ UPtake/ K+ Transporter) transporters, homologous to the bacterial KUP and fungal HAK transporters, which most likely as K+/H+ exchangers function as electrochemical potential-driven transporters. Arabidopsis contains 13 genes, classified into five major clades (Clades I-V). Members of Clade II, including TRH1, are associated with developmental processes. Targeted expression experiments demonstrated that K+ transporter TRH1 is a coupler of two auxin-mediated developmental processes that determine Root System Architecture, root hair morphogenesis and root gravitropism. Targeting TRH1 expression in central cylinder cells that coincide with the acropetal route of auxin transport, rescued trh1 root agravitropism, whereas positional TRH1 expression in peripheral cell layers that define the basipetal route of auxin transport, restored trh1 root hair defects. To dissect the two auxin-mediated developmental responses, a transcriptome analysis was performed identifying the differentially expressed genes involved in either root bending or root hair development.
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Project description:Myosins are evolutionarily conserved motor proteins that interact with actin filaments to regulate organelle transport, cytoplasmic streaming and cell growth. Plant specific Class XI myosin proteins direct cell division and root organogenesis. However, the roles of Class VIII myosin proteins in plant growth and development are less understood. Here, we investigated the function of an auxin-regulated Class VIII myosin, Arabidopsis thaliana Myosin 1 (ATM1), using genetics and live cell microscopy. ATM1 is a plasmodesmata-localized protein that is enriched in actively dividing cells in the root apical meristem (RAM). Loss of ATM1 function results in impaired primary root growth due to decreased RAM size and reduced cell proliferation in a sugar dependent manner. Examination of stem cell marker line expression in atm1-1 indicated impaired division of the lateral root cap and columella cells and a diminished auxin response. Transcriptome analysis of atm1-1 linked these growth defects to dysregulation of cell cycle and auxin pathway genes. Complementation of ATM1 loss-of- function mutant restored root growth and cell cycle progression in the root meristem. Collectively, these results provide novel evidence that ATM1 functions to influence cell proliferation and differentiation in primary roots in response to auxin and sugar cues.
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Project description:Plant roots can regenerate after complete excision of their tip, including the stem cell niche, but it is not clear what developmental program mediates such repair. Here, we use a combination of lineage tracing, single-cell RNA-seq, and marker analysis to test different models of tissue reassembly. We show that rapid cell-identity transitions lead to the formation of a new stem cell niche from multiple remnant tissues. The transcriptome of regenerating cells prior to stem cell activation resembled that of the embryonic root progenitor, and regeneration defects were more severe in embryonic versus adult root mutants. Furthermore, the signaling domains of the hormones auxin and cytokinin mirrored their embryonic dynamics, and manipulation of both hormones altered the position of new tissues and stem cell niche markers. Our findings suggest that plant organ regeneration resembles the developmental stages of embryonic patterning and is guided by spatial information laid down by complementary hormone domains. 215 single cells isolated from marked stele tissue (either using WOL or AHP6 promoters), before, at 3h, 16h and 46h post root tip decapitation
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Project description:The Arabidopsis Branching Enzyme 1 (BE1) gene encodes a putative glycoside hydrolase involved in carbohydrate metabolism. A partial loss-of-function mutation of the BE1 gene (be1-3 mutant) severely impaired adventitious shoot formation and somatic embryogenesis but not root formation in tissue culture. To gain a better understanding of the molecular mechanism underlying the in vitro plant regeneration defects caused by the BE1 gene mutation, we performed RNA sequencing analysis (RNA-seq) to examine the differential gene expression between WS and be1-3 mutant at dedifferentiation and redifferentiation stages.
2014-02-12 | E-MTAB-4394 | biostudies-arrayexpress
Project description:Plant roots can regenerate after complete excision of their tip, including the stem cell niche, but it is not clear what developmental program mediates such repair. Here, we use a combination of lineage tracing, single-cell RNA-seq, and marker analysis to test different models of tissue reassembly. We show that rapid cell-identity transitions lead to the formation of a new stem cell niche from multiple remnant tissues. The transcriptome of regenerating cells prior to stem cell activation resembled that of the embryonic root progenitor, and regeneration defects were more severe in embryonic versus adult root mutants. Furthermore, the signaling domains of the hormones auxin and cytokinin mirrored their embryonic dynamics, and manipulation of both hormones altered the position of new tissues and stem cell niche markers. Our findings suggest that plant organ regeneration resembles the developmental stages of embryonic patterning and is guided by spatial information laid down by complementary hormone domains.
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