The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation
Supplemental File 2
Supplemental File 4
Supplemental File 5
Supplemental File 6
Supplemental File 8
Supplemental File 9
Supplemental File 10
MacPherson, Cameron Ross
Hannah, Matthew A
Bajic, Vladimir B.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
MetadataShow full item record
AbstractBackground: Over application of phosphate fertilizers in modern agriculture contaminates waterways and disrupts natural ecosystems. Nevertheless, this is a common practice among farmers, especially in developing countries as abundant fertilizers are believed to boost crop yields. The study of plant phosphate metabolism and its underlying genetic pathways is key to discovering methods of efficient fertilizer usage. The work presented here describes a genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation.Results: Genome-wide profiling by micro- and tiling-arrays (accessible from GEO: GSE34004) revealed minimal overlap between root and shoot transcriptomes suggesting two independent phosphate-starvation regulons. Novel gene expression patterns were detected for over 1000 candidates and were classified as either initial, persistent, or latent responders. Comparative analysis to AtGenExpress identified cohorts of genes co-regulated across multiple stimuli. The hormone ABA displayed a dominant role in regulating many phosphate-responsive candidates. Analysis of co-regulation enabled the determination of specific versus generic members of closely related gene families with respect to phosphate-starvation. Thus, among others, we showed that PHR1-regulated members of closely related phosphate-responsive families (PHT1;1, PHT1;7-9, SPX1-3, and PHO1;H1) display greater specificity to phosphate-starvation than their more generic counterparts. Conclusion: Our results uncover much larger, staged responses to phosphate-starvation than previously described. To our knowledge, this work describes the most complete genome-wide data on plant nutrient stress to-date. 2012 Woo et al.; licensee BioMed Central Ltd.
CitationWoo J, MacPherson C, Liu J, Wang H, Kiba T, et al. (2012) The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation. BMC Plant Biol 12: 62. doi:10.1186/1471-2229-12-62.
JournalBMC Plant Biology
PubMed Central IDPMC3520718
The following license files are associated with this item:
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- Transcript profiling of cytokinin action in Arabidopsis roots and shoots discovers largely similar but also organ-specific responses.
- Authors: Brenner WG, Schmülling T
- Issue date: 2012 Jul 23
- The transcription factor PHR1 plays a key role in the regulation of sulfate shoot-to-root flux upon phosphate starvation in Arabidopsis.
- Authors: Rouached H, Secco D, Arpat B, Poirier Y
- Issue date: 2011 Jan 24
- Root Cell-Specific Regulators of Phosphate-Dependent Growth.
- Authors: Linn J, Ren M, Berkowitz O, Ding W, van der Merwe MJ, Whelan J, Jost R
- Issue date: 2017 Jul
- Arabidopsis Pht1;5 mobilizes phosphate between source and sink organs and influences the interaction between phosphate homeostasis and ethylene signaling.
- Authors: Nagarajan VK, Jain A, Poling MD, Lewis AJ, Raghothama KG, Smith AP
- Issue date: 2011 Jul
- A central regulatory system largely controls transcriptional activation and repression responses to phosphate starvation in Arabidopsis.
- Authors: Bustos R, Castrillo G, Linhares F, Puga MI, Rubio V, Pérez-Pérez J, Solano R, Leyva A, Paz-Ares J
- Issue date: 2010 Sep 9
Showing items related by title, author, creator and subject.
Plant-specific Histone Deacetylases HDT½ Regulate GIBBERELLIN 2-OXIDASE 2 Expression to Control Arabidopsis Root Meristem Cell NumberLi, Huchen; Torres-Garcia, Jesus; latrasse, David; Benhamed, Moussa; Schilderink, Stefan; Zhou, Wenkun; Kulikova, Olga; Hirt, Heribert; Bisseling, Ton (American Society of Plant Biologists (ASPB), 2017-08-31)Root growth is modulated by environmental factors and depends on cell production in the root meristem (RM). New cells in the meristem are generated by stem cells and transit-amplifying cells, which together determine RM cell number. Transcription factors and chromatin-remodelling factors have been implicated in regulating the switch from stem cells to transit-amplifying cells. Here we show that two Arabidopsis thaliana paralogs encoding plant-specific histone deacetylases, HDT1 and HDT2, regulate a second switch from transit-amplifying cells to expanding cells. Knockdown of HDT½ (hdt1,2i) results in an earlier switch and causes a reduced RM cell number. Our data show that HDT½ negatively regulate the acetylation level of the C19-GIBBERELLIN 2-OXIDASE 2 (GA2ox2) locus and repress the expression of GA2ox2 in the RM and elongation zone. Overexpression of GA2ox2 in the RM phenocopies the hdt1,2i phenotype. Conversely, knockout of GA2ox2 partially rescues the root growth defect of hdt1,2i. These results suggest that by repressing the expression of GA2ox2, HDT½ likely fine-tune gibberellin metabolism and they are crucial for regulating the switch from cell division to expansion to determine RM cell number. We propose that HDT½ function as part of a mechanism that modulates root growth in response to environmental factors.
Characterization of Plant Growth under Single-Wavelength Laser Light Using the Model Plant Arabidopsis ThalianaOoi, Amanda (2016-12)Indoor horticulture offers a promising solution for sustainable food production and is becoming increasingly widespread. However, it incurs high energy and cost due to the use of artificial lighting such as high-pressure sodium lamps, fluorescent light or increasingly, the light-emitting diodes (LEDs). The energy efficiency and light quality of currently available lighting is suboptimal, therefore less than ideal for sustainable and cost-effective large-scale plant production. Here, we demonstrate the use of high-powered single-wavelength lasers for indoor horticulture. Lasers are highly energy-efficient and can be remotely guided to the site of plant growth, thus reducing on-site heat accumulation. Besides, laser beams can be tailored to match the absorption profiles of different plants. We have developed a prototype laser growth chamber and demonstrate that laser-grown plants can complete a full growth cycle from seed to seed with phenotypes resembling those of plants grown under LEDs. Importantly, the plants have lower expression of proteins diagnostic for light and radiation stress. The phenotypical, biochemical and proteomic data show that the singlewavelength laser light is suitable for plant growth and therefore, potentially able to unlock the advantages of this next generation lighting technology for highly energy-efficient horticulture. Furthermore, stomatal movement partly determines the plant productivity and stress management. Abscisic acid (ABA) induces stomatal closure by promoting net K+-efflux from guard cells through outwardrectifying K+ (K+ out) channels to regulate plant water homeostasis. Here, we show that the Arabidopsis thaliana guard cell outward-rectifying K+ (ATGORK) channel is a direct target for ABA in the regulation of stomatal aperture and hence gas exchange and transpiration. Addition of (±)-ABA, but not the biologically inactive (−)-isomer, increases K+ out channel activity in Vicia faba guard cell protoplast. A similar ABA-modulated K+ channel conductance was observed when ATGORK was heterologously expressed in human embryonic kidney 293 (HEK-293) cells. Alignment of ATGORK with known PYR/PYL/RCARs ABA receptors revealed that ATGORK harbors amino acid residues that are similar to those at the latchlike region of the ABA-binding sites. In ATGORK, the double mutations K559A and Y562A at the predicted ABA-interacting site impaired ABA-dependent channel activation and reduced the affinity for ABA in vitro.
Ethylene signalling is involved in regulation of phosphate starvation-induced gene expression and production of acid phosphatases and anthocyanin in ArabidopsisLei, Mingguang; Zhu, Chuanmei; Liu, Yidan; Karthikeyan, Athikkattuvalasu S.; Bressan, Ray Anthony; Raghothama, Kashchandra G.; Liu, Dong (Wiley-Blackwell, 2010-11-30)With the exception of root hair development, the role of the phytohormone ethylene is not clear in other aspects of plant responses to inorganic phosphate (Pi) starvation. The induction of AtPT2 was used as a marker to find novel signalling components involved in plant responses to Pi starvation. Using genetic and chemical approaches, we examined the role of ethylene in the regulation of plant responses to Pi starvation. hps2, an Arabidopsis mutant with enhanced sensitivity to Pi starvation, was identified and found to be a new allele of CTR1 that is a key negative regulator of ethylene responses. 1-aminocyclopropane-1-carboxylic acid (ACC), the precursor of ethylene, increases plant sensitivity to Pi starvation, whereas the ethylene perception inhibitor Ag+ suppresses this response. The Pi starvation-induced gene expression and acid phosphatase activity are also enhanced in the hps2 mutant, but suppressed in the ethylene-insensitive mutant ein2-5. By contrast, we found that ethylene signalling plays a negative role in Pi starvation-induced anthocyanin production. These findings extend the roles of ethylene in the regulation of plant responses to Pi starvation and will help us to gain a better understanding of the molecular mechanism underlying these responses. © 2010 The Authors. New Phytologist © 2010 New Phytologist Trust.