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Redundancies in low K signaling of neo-tetraploids leads in increased shoot K [RNA-seq_1]

ABSTRACT: Whole Genome Duplication (WGD) events occurred frequently during land plant evolution and their long term benefits to neo-functionalization of genes and speciation is well known (Baduel et al., 2018). However short term benefits, important for the establishment of a new population, are more difficult to observe until Chao et al., 2013 described a fitness advantage under high salinity. Additionally shoot K levels were higher in neo-tetraploids, an important feature since K uptake becomes increasingly more difficult on highly saline soil. The molecular basis for these phenotypes was not known. Here we analyze neo-tetraploid Arabidopsis thaliana plants using RNAseq and ICP-MS to evaluate the effect of mutations and ploidy on the gene expression and shoot ionome. We are able to show that neo-tetraploid plants induce low-potassium (K) signaling to increase their shoot K content. However, we also show that this low-K signaling is distinct form previously studied, externally applied low-K signaling. In this way, we are able to identify new components of the K homeostasis network, which are required to regulate K demand. Additionally we are able to show that while individual components of the K uptake system are not sufficient to increase shoot K, a loss of root hairs abolished the ploidy K phenotype (PPP) as does a defective Casparian strip. Root hairs are the site of entry of K into the root and neo-tetraploids increase their root hair length and density (RHI) to facilitate their higher K demand. The Casparian strip on the other hand enables higher K concentration in the stele of the root, which is required for the increased K content in neo-tetraploids.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE180004 | GEO | 2022/07/31

REPOSITORIES: GEO

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Redundancies in low K signaling of neo-tetraploids leads in increased shoot K [RNA-seq_2]

Project description:Whole Genome Duplication (WGD) events occurred frequently during land plant evolution and their long term benefits to neo-functionalization of genes and speciation is well known (Baduel et al., 2018). However short term benefits, important for the establishment of a new population, are more difficult to observe until Chao et al., 2013 described a fitness advantage under high salinity. Additionally shoot K levels were higher in neo-tetraploids, an important feature since K uptake becomes increasingly more difficult on highly saline soil. The molecular basis for these phenotypes was not known. Here we analyze neo-tetraploid Arabidopsis thaliana plants using RNAseq and ICP-MS to evaluate the effect of mutations and ploidy on the gene expression and shoot ionome. We are able to show that neo-tetraploid plants induce low-potassium (K) signaling to increase their shoot K content. However, we also show that this low-K signaling is distinct form previously studied, externally applied low-K signaling. In this way, we are able to identify new components of the K homeostasis network, which are required to regulate K demand. Additionally we are able to show that while individual components of the K uptake system are not sufficient to increase shoot K, a loss of root hairs abolished the ploidy K phenotype (PPP) as does a defective Casparian strip. Root hairs are the site of entry of K into the root and neo-tetraploids increase their root hair length and density (RHI) to facilitate their higher K demand. The Casparian strip on the other hand enables higher K concentration in the stele of the root, which is required for the increased K content in neo-tetraploids.

2022-07-31 | GSE180818 | GEO

Endodermis-specific Receptor-like Kinase (ERK1) is required for the deposition of lignin in the Casparian strip in the root

Project description:The Casparian strip constitutes a physical diffusion barrier formed by the polar deposition of lignin in the root endodermis. The polar deposition of lignin is thought to be mediated by the scaffolding activity of membrane bound Casparian Strip domain proteins (CASPs) and the dirigent domain-containing protein Enhanced Suberin1 (ESB1). Here, we show that the endodermis-specific receptor-like kinase (ERK1), is part of this machinery, playing an essential role in the localization of CASP proteins and in the deposition of lignin, which ultimately are required for the formation of afunctional Casparian strip. ERK1 is localized to the cytoplasm and nucleus of the endodermis, and is part of a signalling pathway that implicates the circadian clock regulator Time for Coffee (TIC). In addition, we found that loss of ERK1 and TIC disrupts the Casparian strip organisation and alters composition of the root microbiome.

2021-09-08 | PXD013861 | Pride

MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root

Project description:Stem cells are defined by their ability to self-renew and produce daughter cells that proliferate and mature. These maturing cells transition from a proliferative state to a terminal state through the process of differentiation. In the Arabidopsis thaliana root the transcription factors SCARECROW and SHORTROOT regulate specification of the bi-potent stem cell that gives rise to the cortical and endodermal progenitors. Subsequent progenitor proliferation and differentiation generates mature endodermis, marked by the Casparian Strip: a cell wall modification that prevents ion diffusion into and out of the vasculature. We identified a transcription factor, MYB36 that regulates the transition from proliferation to differentiation in the endodermis. We show that SCARECROW directly activates MYB36 expression, which in turn directly regulates essential Casparian Strip formation genes. In addition, MYB36 represses extra divisions within the endodermis. Our results demonstrate that MYB36 is a critical positive regulator of differentiation and negative regulator of cell proliferation. 12 samples analyzed: 3 biological replicates each from 1) wild type (Col-0) whole root, 2) mutant (myb36-1) whole root, 3) wild type (Col-0) sorted endodermis, 4) mutant (myb36-1) sorted endodermis

2015-07-20 | E-GEOD-70584 | biostudies-arrayexpress

MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root

2015-07-20 | GSE70584 | GEO

Phosphoproteomic analyses the tetraploid Citrus wilsonii enhanced drought tolerance

Project description:In this study, 17 plants of tetraploid “Zhique” were firstly identified by screening 570 natural seedlings of Citrus wilsonii Tanaka. These tetraploid plants showed different morphology and exhibited significantly increased drought tolerance than the diploids via determination of leaf water potential, relative water content and electrolyte leakage. Large number of genes involved in photosynthesis-responsive were differentially expressed in tetraploids under drought stress by global transcriptome analysis, which was consistent with the detection of photosynthesis indicator including photosynthetic rate, stomatal conductance, chlorophyll and so on. Compared with diploids, phosphorylation modification also plays an important role in the tetraploids after drought stress through the transcriptional and protein level analysis. Additionally, the genes involved in the phenylpropanoid biosynthesis and starch and sucrose metabolism pathways were enriched in both tetraploids and diploids in response to water deficient. Importantly, tetraploids significantly take priority over the diploid via regulating plant hormone signal transduction, especially improving the levels of 3-indoleacetic acid, abscisic acid and salicylic acid and reducing gibberellic A3 and jasmonic acid contents. Collectively, our data reveals that synergistic regulation photosynthesis, phosphorylation modification and plant hormones accumulation contribute to drought tolerance of autotetraploid in Citrus wilsonii.

2022-06-09 | PXD031236 | Pride

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

Gene expression in diploid and evolved tetraploid RPE-1 and BJ-1 cells

Project description:Both diploid RPE-1 and BJ-1 cells were made tetraploid by transient treatment with the cytokinesis inhibitor DCD. Proliferating tetraploids from both BJ-1 and RPE-1 were selected and isolated. The gene expression profiles of the proliferating tetraploid cells were then compared to the diploids from which they originated.

2014-05-22 | GSE57864 | GEO

Scaling of cellular processes with ploidy

Project description:While most eukaryotic cells are diploid, with two chromosome sets, variances in ploidy are common. Despite the relative prevalence of ploidy changes and their relevance for pathology and evolution, a complete picture of consequences of altered ploidy is missing. We analyzed transcriptome and proteome changes in budding yeast Saccharomyces cerevisiae from haploid to tetraploid and found that the mRNA and protein abundance increases linearly with ploidy, but does not double with doubling the DNA content. Besides this linear increase, we found that pathways related to mitochondria and to cytoplasmic ribosomes and translation are differentially regulated. Indeed, with increasing ploidy the cells reduce mitochondrial content and this effect can be rescued by antioxidants. Moreover, cells of higher ploidy reduce their ribosome content while maintaining constant translational output. We show that this is an active process regulated via the Tor1 and Sch9 kinases and a transcriptional corepressor of rDNA transcription, Tup1. Similarly, human tetraploid cells downregulate their ribosome content via Tle1, a Tup1 homolog, demonstrating that the proteome remodeling is a conserved response to increased ploidy.

2022-08-15 | PXD022605 | Pride

Gene expression in diploid and evolved tetraploid RPE-1 and BJ-1 cells

2014-05-22 | E-GEOD-57864 | biostudies-arrayexpress

Differential expression analysis of haploid, diploid, and tetraploid yeast experimentally evolved in raffinose medium

Project description:Haploid, diploid, and tetraploid yeast were experimentally evolved in 2% raffinose medium. After 250 generations, we assessed the gene expression alterations in 2 evolved haploids, 2 evolved diploids, and 4 evolved tetraploids relative to the diploid ancestor.

2017-10-04 | GSE95069 | GEO

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