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NAKR1 deletion analysis

ABSTRACT: ABSTRACT:The SODIUM POTASSIUM ROOT DEFECTIVE 1 (NaKR1) encodes a soluble metal binding protein that is specifically expressed in companion cells of the phloem. The nakr1-1 mutant phenotype includes high Na+, K+, Rb+ and starch accumulation in leaves, short roots, late flowering and decreased long-distance transport of sucrose. Using traditional and DNA microarray-based mapping, a 7 bp deletion was found in an exon of NaKR1 that caused a premature stop. The mutant phenotypes were complemented by the native gene and by GFP and GUS fusions driven by the native promoter. NAKR1-GFP was mobile in the phloem, it moved into sieve elements and into a novel symplasmic domain of the root meristem. Grafting experiments revealed that the high Na+ accumulation was due primarily to loss of NaKR1 function in the leaves. This supports a role for the phloem in recirculating Na+ to the roots to limit Na+ accumulation in leaves. The onset of root phenotypes coincided with NaKR1 expression after germination. Short root length was primarily due to a decrease in cell division rate in the root meristem indicating a role for NaKR1 expression in the phloem in root meristem maintenance.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE24385 | GEO | 2010/12/23

SECONDARY ACCESSION(S): PRJNA132871

REPOSITORIES: GEO

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NAKR1 deletion analysis

Project description:ABSTRACT:The SODIUM POTASSIUM ROOT DEFECTIVE 1 (NaKR1) encodes a soluble metal binding protein that is specifically expressed in companion cells of the phloem. The nakr1-1 mutant phenotype includes high Na+, K+, Rb+ and starch accumulation in leaves, short roots, late flowering and decreased long-distance transport of sucrose. Using traditional and DNA microarray-based mapping, a 7 bp deletion was found in an exon of NaKR1 that caused a premature stop. The mutant phenotypes were complemented by the native gene and by GFP and GUS fusions driven by the native promoter. NAKR1-GFP was mobile in the phloem, it moved into sieve elements and into a novel symplasmic domain of the root meristem. Grafting experiments revealed that the high Na+ accumulation was due primarily to loss of NaKR1 function in the leaves. This supports a role for the phloem in recirculating Na+ to the roots to limit Na+ accumulation in leaves. The onset of root phenotypes coincided with NaKR1 expression after germination. Short root length was primarily due to a decrease in cell division rate in the root meristem indicating a role for NaKR1 expression in the phloem in root meristem maintenance. 3 hybridizations each of mutant NAKR1 and wildtype for deletion identification.

2010-12-23 | E-GEOD-24385 | biostudies-arrayexpress

Vascular rays mediate radial assimilate transport in tuberous roots of Manihot esculenta

Project description:Cassava (Manihot esculenta) is one of the most important staple food crops worldwide. Its starchy tuberous roots supply over 800 million people with carbohydrates. Yet, surprisingly little is known about the processes involved in filling of those vital storage organs. A better understanding of cassava carbohydrate allocation and starch storage is key to improve storage root yield. In this work, we studied cassava morphology and phloem sap flow from source to sink using transgenic pAtSUC2::GFP plants, the phloem tracers esculin and 5(6)-carboxyfluorescein diacetate (CFDA), as well as several staining techniques. We show that cassava performs apoplasmic phloem loading in source leaves and symplasmic unloading into phloem parenchyma cells of tuberous roots. We demonstrate that vascular rays play an important role in radial transport from the phloem to xylem parenchyma cells in tuberous roots. Furthermore, enzymatic and proteomic measurements of storage root tissues confirmed high abundance and activity of enzymes involved in the sucrose synthase-mediated pathway and indicated that starch is stored most efficiently in the outer xylem layers of tuberous roots. Our findings represent a first basis for biotechnological approaches aimed at improved phloem loading and enhanced carbohydrate allocation and storage in order to increase tuberous root yield of cassava.

2019-07-08 | PXD014001 | Pride

Baxter_etal_esb1_mapping

Project description:ABSTRACT: Background: Though central to our understanding of how roots perform their vital function of scavenging water and solutes from the soil, no direct genetic evidence currently exists to support the foundational model that suberin acts to form a chemical barrier limiting the extracellular, or apoplastic, transport of water and solutes in plant roots. Methodologies/Principle Findings: Using the newly characterized enhanced suberin1 (esb1) mutant, we established a connection in Arabidopsis thaliana between suberin in the root, and both water movement through the plant, and solute accumulation in the shoot. Esb1 mutants, characterized by increased root suberin, were found to have reduced day time transpiration rates, and increased water use efficiency during their vegetative growth period. Furthermore, these changes in suberin and water transport were associated with decreases in the accumulation of Ca, Mn and Zn, and increases in the accumulation of Na, S, K, As, Se and Mo in the shoot. Conclusions/Significance: Here we present direct genetic evidence establishing that suberin in the roots plays a critical role in controlling both water and mineral ion uptake and transport to the leaves. The changes observed in the elemental accumulation in leaves are also interpreted as evidence that a significant component of the radial root transport of Ca, Mn and Zn occurs in the apoplast. Keywords: genomic hybridization bulked segregant analysis

2009-04-14 | GSE15655 | GEO

The leaves of creeping bentgrass (Agrostis stolonifera) LC−ESI−MS/MS

Project description:The global emergence of soil salinization poses a serious challenge to many countries and regions. γ-Aminobutyric acid (GABA) is involved in systemic regulation of plant adaptation to salt stress, but the underling molecular and metabolic mechanism still remains largely unknown. The elevated endogenous GABA level by exogenous application of GABA could significantly improve salt tolerance in creeping bentgrass with the enhancement of antioxidant capacity, photosynthetic characteristics, osmotic adjustment (OA), and water use efficiency. GABA strongly upregulated transcript levels of AsPPa2, AsATPaB2, AsNHX2/4/6, and AsSOS1/20 in roots involved in enhanced capacity of Na+ compartmentalization and mitigation of Na+ toxicity in cytosol. Significant downregulation of AsHKT1/4 expression could be induced by GABA in leaves in relation to maintenance of significantly lower Na+ accumulation and higher K+/Na+ ratio. GABA-depressed aquaporins (AQPs) expression and accumulation induced declines in stomatal conductance and transpiration, thereby reducing water loss in leaves during salt stress. For metabolic regulation, GABA primarily enhanced sugars and amino acids accumulation and metabolism largely contributing to improved salt tolerance through maintaining OA and metabolic homeostasis. Other major pathways could be responsible for GABA-induced salt tolerance including increases in antioxidant defense, heat shock proteins, dehydrins, and myo-inositol accumulation in leaves. Integrative analyses of molecular, protein, metabolic, and physiological changes reveal systemic function of GABA on regulating ions, water, and metabolic homeostasis in non-halophytic creeping bentgrass under salt stress.

2020-01-13 | PXD015066 | Pride

Genome-wide analysis of SHORTROOT targets in the Arabidopsis root stele

Project description:Asymmetric cell division (ACD) and positional signals play critical roles in the tissue patterning during multicellular organ development. In the Arabidopsis root meristem, two major phloem cell types arise via ACDs of distinct origins: one for companion cells and the other for proto- and metaphloem sieve elements. The molecular mechanisms underlying each of these processes have been reported, however, how these two are coordinated has remained elusive. Here, we report that SHORTROOT (SHR) is the key coordinator of two ACD processes for phloem development. SHR moving into the endodermis regulates ACD for companion cells by turning on microRNA165/6. ACD that generates phloem sieve elements is mediated by SHR moving into phloem precursors. To find the downstream targets of SHR in the stele, pCRE1::erGFP was introduced into wild type and shr-2 backgrounds to express GFP in the stele cells in the root meristem. We then collected GFP-expressing stele cells from the wild type, shr-2 and pCRE1::SHRΔNLELDV:nlsGFP; shr-2 through Fluorescence Activated Cell Sorter (FACS). RNAs were extracted from the sorted cells of each line and processed for generating labeled probes to be hybridized onto GeneChip Arabidopsis Tiling 1.0R Array (Affymetrix). We then examined the influence of SHR on phloem enriched genes in the tiling array data. In this analysis, we found 224 genes that are down-regulated in shr-2 in comparison to the wild type and then restore expression in pCRE1::SHRΔNLELDV:nlsGFP; shr-2.

2019-08-01 | GSE130061 | GEO

Small RNAs in different tissues and phloem of oilseed rape under nutrient stress conditions

Project description:The objective of this study was to identify nutrient-responsive small RNAs in different tissues and in phloem sap of rape plants. miRNA microarrays containing all currently known plant miRNAs (Sanger miRBase versions 10.0, 10.1 and 11.0), and a set of unknown small RNAs cloned earlier from Brassica phloem sap (Bn_PsRNA) were used. The phloem, leaf and root response to nutrient deficiency were analyzed by removing either sulfate, copper or iron from the growth medium. The small RNA profile from phloem and inflorescence stems of plants grown under full nutrition conditions was also analyzed and compared. The study demonstrates that the phloem sap sRNA profile is distinct from that of the inflorescence stems, leaves and roots. Furthermore, we could identify phloem-enriched small RNAs and showed that some of them specifically accumulate in the phloem in response to nutrient deprivation.

2010-02-24 | GSE20263 | GEO

Global transcriptome analysis identifies genes regulated by FT in the leaf

Project description:Flowering of Arabidopsis thaliana is accelerated by several environmental cues, including exposure to long days. The photoperiod-dependent promotion of flowering involves the transcriptional induction of FLOWERING LOCUS T (FT) in the phloem of the leaf. FT encodes a mobile protein that is transported from the leaves to the shoot apical meristem, where it forms part of a regulatory complex that induces flowering. Whether FT also has biological functions in leaves of wild-type plants remains unclear. In order to address this issue, we first studied the leaf transcriptomic changes associated with its over expression in the companion cells of the phloem. To this end, transgenic A. thaliana plants that misexpress FT from the pGAS1 promoter in a ft-10 tsf-1 double mutant background were employed (pGAS1:FT ft-10 tsf-1). In these transgenic plants, the use of the pGAS1 promoter ensures that the FT transgene is expressed in phloem companion cells of the minor veins, recreating the spatial pattern of expression described for the native gene. In this studuy, the transcriptome of leaves of pGAS1:FT ft-10 tsf-1 transgenic plants was compared to that of ft-10 tsf-1 and Col-0 plants using Tiling Arrays.

2020-02-05 | GSE125054 | GEO

Single-Cell RNA-seq analysis of cell lineages in De Novo Root Regeneration

Project description:Detached Arabidopsis leaves can regenerate adventitious roots, providing a platform to study de novo root regeneration (DNRR). We performed single-cell RNA-seq analysis and revealed that regeneration primarily originated from vascular stem-cell organizer within procambium, followed by step-by-step changes of transcriptome in cell fate transition, including gradually erasing the vascular stem-cell organizer identity and recruiting the root development program.

2022-02-10 | GSE147289 | GEO

Shoot-to-root mobile CEPD-like 2 integrates shoot nitrogen status to systemically regulate nitrate uptake in Arabidopsis

Project description:Plants modulate the efficiency of root nitrogen (N) acquisition in response to shoot N demand. However, molecular components directly involved in this shoot-to-root communication remain to be identified. Here, we show that phloem-mobile CEPD-like 2 (CEPDL2) polypeptide is upregulated in the leaf vasculature in response to decreased shoot N status and, after translocation to the roots, promotes high-affinity uptake and root-to-shoot transport of nitrate by activating nitrate transporter genes such as NRT2.1, NRT3.1 and NRT1.5. Loss of CEPDL2 decreases nitrate uptake and root-to-shoot transport activity in roots, leading to a reduction in shoot nitrate content and plant biomass. CEPDL2 contributes to N acquisition cooperatively with CEPD1 and CEPD2 that mediate root N status, and their complete loss severely impairs N homeostasis in plants. Reciprocal grafting analysis provided conclusive evidence that the shoot CEPDL2/CEPD genotype defines the root high-affinity uptake activity of nitrate. Our results indicate that plants integrate shoot N status and root N status in leaves and systemically regulate the efficiency of root N acquisition.

2020-02-10 | GSE140834 | GEO

Transcriptomics of lateral root initiation in Maize

Project description:We developed a method to synchronize the induction of lateral roots in primary and adventitious roots of Zea mays, and used it to perform a genome-wide transcriptome analysis of the pericycle cells in front of the phloem poles during lateral root initiation.

2013-07-16 | GSE45691 | GEO

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