Publications by authors named "Prakash P Kumar"

58 Publications

Ethylene-Mediated Modulation of Bud Phenology, Cold Hardiness, and Hormone Biosynthesis in Peach ().

Plants (Basel) 2021 Jun 22;10(7). Epub 2021 Jun 22.

Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Tech, School of Plant and Environmental Sciences, Winchester, VA 22602, USA.

Spring frosts exacerbated by global climate change have become a constant threat to temperate fruit production. Delaying the bloom date by plant growth regulators (PGRs) has been proposed as a practical frost avoidance strategy. Ethephon is an ethylene-releasing PGR found to delay bloom in several fruit species, yet its use is often coupled with harmful effects, limiting its applicability in commercial tree fruit production. Little information is available regarding the mechanisms by which ethephon influences blooming and bud dormancy. This study investigated the effects of fall-applied ethephon on bud phenology, cold hardiness, and hormonal balance throughout the bud dormancy cycle in peach. Our findings concluded that ethephon could alter several significant aspects of peach bud physiology, including accelerated leaf fall, extended chilling accumulation period, increased heat requirements, improved cold hardiness, and delayed bloom date. Ethephon effects on these traits were primarily dependent on its concentration and application timing, with a high concentration (500 ppm) and an early application timing (10% leaf fall) being the most effective. Endogenous ethylene levels were induced significantly in the buds when ethephon was applied at 10% versus 90% leaf fall, indicating that leaves are essential for ethephon uptake. The hormonal analysis of buds at regular intervals of chilling hours (CH) and growing degree hours (GDH) also indicated that ethephon might exert its effects through an abscisic acid (ABA)-independent way in dormant buds. Instead, our data signifies the role of jasmonic acid (JA) in mediating budburst and bloom in peach, which also appears to be influenced by ethephon treatment. Overall, this research presents a new perspective in interpreting horticultural traits in the light of biochemical and molecular data and sheds light on the potential role of JA in bud dormancy, which deserves further attention in future studies that aim at mitigating spring frosts.
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http://dx.doi.org/10.3390/plants10071266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8309013PMC
June 2021

WRKY9 transcription factor regulates cytochrome P450 genes CYP94B3 and CYP86B1, leading to increased root suberin and salt tolerance in Arabidopsis.

Physiol Plant 2021 Jul 12;172(3):1673-1687. Epub 2021 Mar 12.

Department of Biological Sciences, National University of Singapore, Singapore, Singapore.

Salinity affects crop productivity worldwide and mangroves growing under high salinity exhibit adaptations such as enhanced root apoplastic barrier to survive under such conditions. We have identified two cytochrome P450 family genes, AoCYP94B3 and AoCYP86B1 from the mangrove tree Avicennia officinalis and characterized them using atcyp94b3 and atcyp86b1, which are mutants of their putative Arabidopsis orthologs and the corresponding complemented lines with A. officinalis genes. CYP94B3 and CYP86B1 transcripts were induced upon salt treatment in the roots of both A. officinalis and Arabidopsis. Both AoCYP94B3 and AoCYP86B1 were localized to the endoplasmic reticulum. Heterologous expression of 35S::AoCYP94B3 and 35S::AoCYP86B1 in their respective Arabidopsis mutants (atcyp94b3 and atcyp86b1) increased the salt tolerance of the transgenic seedlings by reducing the amount of Na accumulation in the shoots. Moreover, the reduced root suberin phenotype of atcyp94b3 was rescued in the 35S::AoCYP94B3;atcyp94b3 transgenic Arabidopsis seedlings. Gas-chromatography and mass spectrometry analyses showed that the amount of suberin monomers (C-16 ω-hydroxy acids, C-16 α, ω-dicarboxylic acids and C-20 eicosanol) were increased in the roots of 35S::AoCYP94B3;atcyp94b3 Arabidopsis seedlings. Using chromatin immunoprecipitation and electrophoretic mobility shift assays, we identified AtWRKY9 as the upstream regulator of AtCYP94B3 and AtCYP86B1 in Arabidopsis. In addition, atwrky9 showed suppressed expression of AtCYP94B3 and AtCYP86B1 transcripts, and reduced suberin in the roots. These results show that AtWRKY9 controls suberin deposition by regulating AtCYP94B3 and AtCYP86B1, leading to salt tolerance. Our data can be used for generating salt-tolerant crop plants in the future.
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http://dx.doi.org/10.1111/ppl.13371DOI Listing
July 2021

Functional characterization and expression profiling of glyoxalase III genes in date palm grown under abiotic stresses.

Physiol Plant 2021 Jun 27;172(2):780-794. Epub 2020 Oct 27.

Department of Biology, College of Sciences, Sultan Qaboos University, Muscat, Oman.

Methylglyoxal (MG), a by-product of various metabolic processes, including glycolysis, is a highly reactive cytotoxic metabolite. The level of MG in the cell is maintained at a non-toxic level via MG detoxification pathways such as the universal glyoxalase system, including glyoxalase I/II/III enzymes. Glyoxalase III (DJ-1) can breakdown MG to d-lactate in a single step without reducing glutathione (GSH). Elucidating the function of the DJ-1 gene family may provide further knowledge about its role in plants under abiotic stresses. Here, we characterize four glyoxalase III genes (PdDJ-1B1, PdDJ-1B2, PdDJ-1C, and PdDJ-1D) encoding the conserved DJ-1 domain in the genome of the date palm, a crop with high drought and salinity tolerance. The expression level of the PdDJ-1 genes increased in date palm leaves upon salinity treatment. In addition, overexpression of PdDJ-1 genes in Escherichia coli and the complementation in yeast hsp31Δ knockout mutant cells enhanced their growth rate and reduced the accumulation of reactive oxygen species (ROS) under MG and oxidative stress conditions as shown by the flow cytometry assay. Subcellular localization using confocal microscopy revealed the accumulation of PdDJ-1B1, PdDJ-1C, and PdDJ-1D in the chloroplast, whereas PdDJ-1B2 was localized to the cytosol. Remarkably, constitutive expression of the PdDJ-1C gene in Arabidopsis thaliana Columbia (Col-0) resulted in the generation of non-viable albino plants implying that PdDJ-1C plays a critical function in chloroplast development. These findings suggest that PdDJ-1 protein has an important function in MG-detoxification and maintaining the redox balance in date palm plants under abiotic stress conditions.
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http://dx.doi.org/10.1111/ppl.13239DOI Listing
June 2021

Regulation of Expression by bHLH and WRKY Transcription Factors Helps to Confer Increased Salt Tolerance to Plants.

Front Plant Sci 2020 25;11:1311. Epub 2020 Aug 25.

Department of Biological Sciences, National University of Singapore, Singapore, Singapore.

Potassium transporters play an essential role in maintaining cellular ion homeostasis, turgor pressure, and pH, which are critical for adaptation under salt stress. We identified a salt responsive KUP/HAK/KT transporter family gene, , which has high sequence similarity to its ortholog . These genes were functionally characterized in mutant yeast cells and plants. Both and were induced by salt stress, and was primarily induced in roots. Subcellular localization revealed that AoKUP2 and AtKUP2 are localized to the plasma membrane and mitochondria. Expression of and in mutant strain (BY4741 ΔΔ) helped to rescue the growth defect of the mutant under different NaCl and K concentrations. Furthermore, constitutive expression of and conferred enhanced salt tolerance in indicated by higher germination rate, better survival, and increased root and shoot length compared to the untreated controls. Analysis of Na and K contents in the shoots and roots showed that ectopic expression lines accumulated less Na and more K than the WT. Two stress-responsive transcription factors, bHLH122 and WRKY33, were identified as direct regulators of expression. Our results suggest that AtKUP2 plays a key role in enhancing salt stress tolerance by maintaining cellular ion homeostasis.
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http://dx.doi.org/10.3389/fpls.2020.01311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477289PMC
August 2020

Regulation of a Cytochrome P450 Gene by WRKY33 Transcription Factor Controls Apoplastic Barrier Formation in Roots to Confer Salt Tolerance.

Plant Physiol 2020 12 14;184(4):2199-2215. Epub 2020 Sep 14.

Department of Biological Sciences, National University of Singapore, Singapore 117543

Salinity is an environmental stress that causes decline in crop yield. and other mangroves have adaptations such as ultrafiltration at the roots aided by apoplastic cell wall barriers to thrive in saline conditions. We studied a cytochrome P450 gene from , , and its putative ortholog in Arabidopsis (), , which are involved in apoplastic barrier formation. Both genes were induced by 30 min of salt treatment in the roots. Heterologous expression of in the Arabidopsis mutant and wild-type rice () conferred increased NaCl tolerance to seedlings by enhancing root suberin deposition. Histochemical staining and gas chromatography-tandem mass spectrometry quantification of suberin precursors confirmed the role of CYP94B1 in suberin biosynthesis. Using chromatin immunoprecipitation and yeast one-hybrid and luciferase assays, we identified AtWRKY33 as the upstream regulator of in Arabidopsis. In addition, mutants exhibited reduced suberin and salt-sensitive phenotypes, which were rescued by expressing in the background. This further confirmed that AtWRKY33-mediated regulation of is part of the salt tolerance mechanism. Our findings may help efforts aimed at generating salt-tolerant crops.
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http://dx.doi.org/10.1104/pp.20.01054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723105PMC
December 2020

Molecular Characterization of a Date Palm Vascular Highway 1-Interacting Kinase () Under Abiotic Stresses.

Genes (Basel) 2020 05 19;11(5). Epub 2020 May 19.

Department of Biology, College of Sciences, Sultan Qaboos University, P.O. Box 36, Muscat 123, Oman.

The date palm () is an extremophile plant that can adapt to various abiotic stresses including drought and salinity. Salinity tolerance is a complex trait controlled by numerous genes. Identification and functional characterization of salt-responsive genes from the date palm is fundamental to understand salinity tolerance at the molecular level in this plant species. In this study, a salt-inducible vascular highway 1-interacting kinase () that is a MAP kinase kinase kinase (MAPKKK) gene from the date palm, was functionally characterized using in vitro and in vivo strategies. , one of the 597 kinases encoded by the date palm genome possesses an ankyrin repeat domain and a kinase domain. The recombinant PdVIK protein exhibited phosphotyrosine activity against myelin basic protein (MBP) substrate. Overexpression of in yeast significantly improved its tolerance to salinity, LiCl, and oxidative stresses. Transgenic Arabidopsis seedlings overexpressing displayed improved tolerance to salinity, osmotic, and oxidative stresses as assessed by root growth assay. The transgenic lines grown in the soil also displayed modulated salt response, compared to wild-type controls as evaluated by the overall plant growth and proline levels. Likewise, the transgenic lines exhibited drought tolerance by maintaining better relative water content (RWC) compared to non-transgenic control plants. Collectively, these results implicate the involvement of in modulating the abiotic stress response of the date palm.
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http://dx.doi.org/10.3390/genes11050568DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7288329PMC
May 2020

A novel tonoplast Na/H antiporter gene from date palm (PdNHX6) confers enhanced salt tolerance response in Arabidopsis.

Plant Cell Rep 2020 Aug 7;39(8):1079-1093. Epub 2020 May 7.

Department of Biology, College of Sciences, Sultan Qaboos University, P.O. Box 36, 123, Muscat, Oman.

Key Message: A sodium hydrogen exchanger (NHX) gene from the date palm enhances tolerance to salinity in Arabidopsis plants. Plant sodium hydrogen exchangers/antiporters (NHXs) are pivotal regulators of intracellular Na/K and pH homeostasis, which is essential for salt stress adaptation. In this study, a novel orthologue of Na/H antiporter was isolated from date palm (PdNHX6) and functionally characterized in mutant yeast cells and Arabidopsis plants to assess the behavior of the transgenic organisms in response to salinity. Genetically transformed yeast cells with PdNHX6 were sensitive to salt stress when compared to the empty vector (EV) yeast cells. Besides, the acidity value of the vacuoles of the transformant yeast cells has significantly (p ≤ 0.05) increased, as indicated by the calibrated fluorescence intensity measurements and the fluorescence imagining analyses. This observation supports the notion that PdNHX6 might regulate proton pumping into the vacuole, a crucial salt tolerance mechanism in the plants. Consistently, the transient overexpression and subcellular localization revealed the accumulation of PdNHX6 in the tonoplast surrounding the central vacuole of Nicotiana benthamiana leaf epidermal cells. Stable overexpression of PdNHX6 in Arabidopsis plants enhanced tolerance to salt stress and retained significantly higher chlorophyll, water contents, and increased seed germination under salinity when compared to the wild-type plants. Despite the significant increase of Na, transgenic Arabidopsis lines maintained a balanced Na/K ratio under salt stress conditions. Together, the results obtained from this study imply that PdNHX6 is involved in the salt tolerance mechanism in plants by controlling K and pH homeostasis of the vacuoles.
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http://dx.doi.org/10.1007/s00299-020-02549-5DOI Listing
August 2020

An LRR-only protein regulates abscisic acid-mediated abiotic stress responses during Arabidopsis seed germination.

Plant Cell Rep 2020 Jul 10;39(7):909-920. Epub 2020 Apr 10.

Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.

Key Message: LRRop-1, induced by DOF6 transcription factor, negatively regulates abiotic stress responses during Arabidopsis seed germination. The lrrop-1 mutant has reduced ABA signaling, which is part of the underlying stress-remediation mechanism. The large family of leucine-rich repeat (LRR) proteins plays a role in plant immune responses. Most LRR proteins have multiple functional domains, but a subfamily is known to possess only the LRR domain. The roles of these LRR-only proteins in Arabidopsis remain largely uncharacterized. In the present study, we have identified 44 LRR-only proteins in Arabidopsis and phylogenetically classified them into nine sub-groups. We characterized the function of LRRop-1, belonging to sub-group V. LRRop-1 encodes a predominantly ER-localized LRR domain-containing protein that is highly expressed in seeds and rosette leaves. Promoter motif analysis revealed an enrichment in binding sites for several GA-responsive and stress-responsive transcription factors. The lrrop-1 mutant seeds showed enhanced seed germination on medium containing abscisic acid (ABA), paclobutrazol and NaCl compared to the wild type (WT), demonstrating higher abiotic stress tolerance. Also, the lrrop-1 mutant seeds have lower levels of endogenous ABA, but higher levels of gibberellic acid (GA) and jasmonic acid-Ile (JA-Ile) compared to the WT. Furthermore, lrrop-1 mutant seeds imbibed with ABA exhibited reduced expression of ABA-responsive genes compared to similarly treated WT seeds, suggesting suppressed ABA signaling events in the mutant. Furthermore, chromatin immunoprecipitation (ChIP) data showed that DNA BINDING1 ZINC FINGER6 (DOF6), a negative regulator of seed germination, could directly bind to the LRRop-1 promoter and up-regulate its expression. Thus, our results show that LRRop-1 regulates ABA-mediated abiotic stress responses during Arabidopsis seed germination.
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http://dx.doi.org/10.1007/s00299-020-02538-8DOI Listing
July 2020

Systems Metabolic Alteration in a Semi-Dwarf Rice Mutant Induced by Gene Mutation.

Int J Mol Sci 2020 Mar 11;21(6). Epub 2020 Mar 11.

Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore.

Dwarfism and semi-dwarfism are among the most valuable agronomic traits in crop breeding, which were adopted by the "Green Revolution". Previously, we reported a novel semi-dwarf rice mutant () derived from the insertion of a single copy of transposon into the gene . However, the systems metabolic effect of the mutation is not well understood, which is important for understanding the gene function and developing new semi-dwarf mutants. Here, the metabolic phenotypes in the semi-dwarf mutant (M) and ectopic expression (ECE) rice line were compared to the wild-type (WT) rice, by using nuclear magnetic resonance (NMR) metabolomics and quantitative real-time polymerase chain reaction (qRT-PCR). Compared with WT, ECE of the gene resulted in significant increase of γ-aminobutyrate (GABA), glutamine, and alanine, but significant decrease of glutamate, aromatic and branched-chain amino acids, and some other amino acids. The ECE caused significant increase of monosaccharides (glucose, fructose), but significant decrease of disaccharide (sucrose); induced significant changes of metabolites involved in choline metabolism (phosphocholine, ethanolamine) and nucleotide metabolism (adenosine, adenosine monophosphate, uridine). These metabolic profile alterations were accompanied with changes in the gene expression levels of some related enzymes, involved in GABA shunt, glutamate and glutamine metabolism, choline metabolism, sucrose metabolism, glycolysis/gluconeogenesis pathway, tricarboxylic acid (TCA) cycle, nucleotide metabolism, and shikimate-mediated secondary metabolism. The semi-dwarf mutant showed corresponding but less pronounced changes, especially in the gene expression levels. It indicates that gene mutation in rice causes significant alteration in amino acid metabolism, carbohydrate metabolism, nucleotide metabolism, and shikimate-mediated secondary metabolism. The present study will provide essential information for the gene function analysis and may serve as valuable reference data for the development of new semi-dwarf mutants.
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http://dx.doi.org/10.3390/ijms21061924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7139402PMC
March 2020

Expression of AoNHX1 increases salt tolerance of rice and Arabidopsis, and bHLH transcription factors regulate AtNHX1 and AtNHX6 in Arabidopsis.

Plant Cell Rep 2019 Oct 26;38(10):1299-1315. Epub 2019 Jul 26.

Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.

Key Message: Expression of AoNHX1 from the mangrove Avicennia increases salt tolerance of rice and Arabidopsis, and specific bHLH transcription factors regulate AtNHX1 and AtNHX6 in Arabidopsis to mediate the salinity response. Improving crop plants to better tolerate soil salinity is a challenging task. Mangrove trees such as Avicennia officinalis have special adaptations to thrive in high salt conditions, which include subcellular compartmentalization of ions facilitated by specialized ion transporters. We identified and characterized two genes encoding Na/H exchangers AoNHX1 and AoNHX6 from Avicennia. AoNHX1 was present in the tonoplast, while, AoNHX6 was localized to the ER and Golgi. Both NHXs were induced by NaCl treatment, with AoNHX1 showing high expression levels in the leaves and AoNHX6 in the seedling roots. Yeast deletion mutants (ena1-5Δ nha1Δ nhx1Δ and ena1-5Δ nha1Δ vnx1Δ) complemented with AoNHX1 and AoNHX6 showed increased tolerance to both NaCl and KCl. Expression of AoNHX1 and AoNHX6 in the corresponding Arabidopsis mutants conferred enhanced NaCl tolerance. The underlying molecular regulatory mechanism was investigated using AtNHX1 and AtNHX6 in Arabidopsis. We identified two basic helix-loop-helix (bHLH) transcription factors AtMYC2 and AtbHLH122 as the ABA-mediated upstream regulators of AtNHX1 and AtNHX6 by chromatin immunoprecipitation. Furthermore, expression of AtNHX1 and AtNHX6 transcripts was reduced in the atmyc2 and atbhlh122 mutants. Lastly, transgenic rice seedlings harboring pUBI::AoNHX1 showed enhanced salt tolerance, suggesting that this gene can be exploited for developing salt-tolerant crops.
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http://dx.doi.org/10.1007/s00299-019-02450-wDOI Listing
October 2019

Regulation of Seed Germination: The Involvement of Multiple Forces Exerted via Gibberellic Acid Signaling.

Mol Plant 2019 01 21;12(1):24-26. Epub 2018 Dec 21.

Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.molp.2018.12.013DOI Listing
January 2019

OsTPS8 controls yield-related traits and confers salt stress tolerance in rice by enhancing suberin deposition.

New Phytol 2019 02 5;221(3):1369-1386. Epub 2018 Oct 5.

Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore City, 117543, Singapore.

Class I TREHALOSE-PHOSPHATE-SYNTHASE (TPS) genes affect salinity tolerance and plant development. However, the function of class IITPS genes and their underlying mechanisms of action are unknown. We report the identification and functional analysis of a rice class IITPS gene (OsTPS8). The ostps8 mutant was characterised by GC-MS analysis, an abscisic acid (ABA) sensitivity test and by generating transgenic lines. To identify the underlying mechanism, gene expression analyses, genetic complementation and examination of suberin deposition in the roots were conducted. The ostps8 mutant showed salt sensitivity, ABA sensitivity and altered agronomic traits compared to the wild-type (WT), which could be rescued upon complementation. The dsRNAi line phenocopied the mutant, while the overexpression lines exhibited enhanced salt tolerance. The ostps8 mutant showed significantly reduced soluble sugars, Casparian bands and suberin deposition in the roots compared to the WT and overexpression lines. The mutant also showed downregulation of SAPKs (rice SnRK2s) and ABA-responsive genes. Furthermore, ostps8pUBI::SAPK9 rescued the salt-sensitive phenotype of ostps8. Our results suggest that OsTPS8 may regulate suberin deposition in rice through ABA signalling. Additionally, SAPK9-mediated regulation of altered ABA-responsive genes helps to confer salinity tolerance. Overexpression of OsTPS8 was adequate to confer enhanced salinity tolerance without any yield penalty, suggesting its usefulness in rice genetic improvement.
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http://dx.doi.org/10.1111/nph.15464DOI Listing
February 2019

Regulation of Seed Germination and Abiotic Stresses by Gibberellins and Abscisic Acid.

Front Plant Sci 2018 20;9:838. Epub 2018 Jun 20.

Department of Biological Sciences, National University of Singapore, Singapore, Singapore.

Overall growth and development of a plant is regulated by complex interactions among various hormones, which is critical at different developmental stages. Some of the key aspects of plant growth include seed development, germination and plant survival under unfavorable conditions. Two of the key phytohormones regulating the associated physiological processes are gibberellins (GA) and abscisic acid (ABA). GAs participate in numerous developmental processes, including, seed development and seed germination, seedling growth, root proliferation, determination of leaf size and shape, flower induction and development, pollination and fruit expansion. Despite the association with abiotic stresses, ABA is essential for normal plant growth and development. It plays a critical role in different abiotic stresses by regulating various downstream ABA-dependent stress responses. Plants maintain a balance between GA and ABA levels constantly throughout the developmental processes at different tissues and organs, including under unfavorable environmental or physiological conditions. Here, we will review the literature on how GA and ABA control different stages of plant development, with focus on seed germination and selected abiotic stresses. The possible crosstalk of ABA and GA in specific events of the above processes will also be discussed, with emphasis on downstream stress signaling components, kinases and transcription factors (TFs). The importance of several key ABA and GA signaling intermediates will be illustrated. The knowledge gained from such studies will also help to establish a solid foundation to develop future crop improvement strategies.
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http://dx.doi.org/10.3389/fpls.2018.00838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6019495PMC
June 2018

The OsPS1-F gene regulates growth and development in rice by modulating photosynthetic electron transport rate.

Plant Cell Rep 2018 Feb 17;37(2):377-385. Epub 2017 Nov 17.

Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Republic of Singapore.

Key Message: Ds insertion in rice OsPS1-F gene results in semi-dwarf plants with reduced tiller number and grain yield, while genetic complementation with OsPS1-F rescued the mutant phenotype. Photosynthetic electron transport is regulated in the chloroplast thylakoid membrane by multi-protein complexes. Studies about photosynthetic machinery and its subunits in crop plants are necessary, because they could be crucial for yield enhancement in the long term. Here, we report the characterization of OsPS1-F (encoding Oryza sativa PHOTOSYSTEM 1-F subunit) using a single copy Ds insertion rice mutant line. The homozygous mutant (osps1-f) showed striking difference in growth and development compared to the wild type (WT), including, reduction in plant height, tiller number, grain yield as well as pale yellow leaf coloration. Chlorophyll concentration and electron transport rate were significantly reduced in the mutant compared to the WT. OsPS1-F gene was highly expressed in rice leaves compared to other tissues at different developmental stages tested. Upon complementation of the mutant with proUBI::OsPS1-F, the observed mutant phenotypes were rescued. Our results illustrate that OsPS1-F plays an important role in regulating proper growth and development of rice plants.
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http://dx.doi.org/10.1007/s00299-017-2235-8DOI Listing
February 2018

A Novel RGL2-DOF6 Complex Contributes to Primary Seed Dormancy in Arabidopsis thaliana by Regulating a GATA Transcription Factor.

Mol Plant 2017 10 14;10(10):1307-1320. Epub 2017 Sep 14.

Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore. Electronic address:

The DELLA protein RGA-LIKE2 (RGL2) is a key transcriptional repressor of gibberellic acid (GA) signaling that regulates seed germination. We identified GATA12, a gene encoding a GATA-type zinc finger transcription factor, as one of the downstream targets of RGL2 in Arabidopsis thaliana. Our data show that freshly harvested (unstratified) seeds of GATA12 antisense suppression lines have reduced dormancy compared with the wild-type, while ectopic expression lines show enhanced seed dormancy. We show that GATA12 expression is negatively regulated by GA, and its transcript levels decline dramatically under dormancy-breaking conditions such as dry storage and cold stratification of seeds. GATA12 promoter has several GAMYB- and DOF-associated motifs that are known to be GA- and RGL2-responsive, respectively. Chromatin immunoprecipitation assay showed that a protein complex containing RGL2 can bind to GATA12 promoter and thereby regulate its expression. RGL2 lacks a DNA binding domain and requires a transcription factor to induce GATA12 expression. Our data show that this RGL2-containing protein complex includes DNA BINDING1 ZINC FINGER6 (DOF6), which is a known negative regulator of germination in freshly harvested seeds. We further show that this novel RGL2-DOF6 complex is required for activating GATA12 expression, thus revealing a molecular mechanism to enforce primary seed dormancy.
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http://dx.doi.org/10.1016/j.molp.2017.09.004DOI Listing
October 2017

Transcriptomics analysis of salt stress tolerance in the roots of the mangrove Avicennia officinalis.

Sci Rep 2017 08 30;7(1):10031. Epub 2017 Aug 30.

Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.

Salinity affects growth and development of plants, but mangroves exhibit exceptional salt tolerance. With direct exposure to salinity, mangrove roots possess specific adaptations to tolerate salt stress. Therefore, studying the early effects of salt on mangrove roots can help us better understand the tolerance mechanisms. Using two-month-old greenhouse-grown seedlings of the mangrove tree Avicennia officinalis subjected to NaCl treatment, we profiled gene expression changes in the roots by RNA-sequencing. Of the 6547 genes that were differentially regulated in response to salt treatment, 1404 and 5213 genes were significantly up- and down-regulated, respectively. By comparative genomics, 93 key salt tolerance-related genes were identified of which 47 were up-regulated. Upon placing all the differentially expressed genes (DEG) in known signaling pathways, it was evident that most of the DEGs involved in ethylene and auxin signaling were up-regulated while those involved in ABA signaling were down-regulated. These results imply that ABA-independent signaling pathways also play a major role in salt tolerance of A. officinalis. Further, ethylene response factors (ERFs) were abundantly expressed upon salt treatment and the Arabidopsis mutant aterf115, a homolog of AoERF114 is characterized. Overall, our results would help in understanding the possible molecular mechanism underlying salt tolerance in plants.
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http://dx.doi.org/10.1038/s41598-017-10730-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5577154PMC
August 2017

Plant hormone-mediated regulation of stress responses.

BMC Plant Biol 2016 Apr 14;16:86. Epub 2016 Apr 14.

Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.

Background: Being sessile organisms, plants are often exposed to a wide array of abiotic and biotic stresses. Abiotic stress conditions include drought, heat, cold and salinity, whereas biotic stress arises mainly from bacteria, fungi, viruses, nematodes and insects. To adapt to such adverse situations, plants have evolved well-developed mechanisms that help to perceive the stress signal and enable optimal growth response. Phytohormones play critical roles in helping the plants to adapt to adverse environmental conditions. The elaborate hormone signaling networks and their ability to crosstalk make them ideal candidates for mediating defense responses.

Results: Recent research findings have helped to clarify the elaborate signaling networks and the sophisticated crosstalk occurring among the different hormone signaling pathways. In this review, we summarize the roles of the major plant hormones in regulating abiotic and biotic stress responses with special focus on the significance of crosstalk between different hormones in generating a sophisticated and efficient stress response. We divided the discussion into the roles of ABA, salicylic acid, jasmonates and ethylene separately at the start of the review. Subsequently, we have discussed the crosstalk among them, followed by crosstalk with growth promoting hormones (gibberellins, auxins and cytokinins). These have been illustrated with examples drawn from selected abiotic and biotic stress responses. The discussion on seed dormancy and germination serves to illustrate the fine balance that can be enforced by the two key hormones ABA and GA in regulating plant responses to environmental signals.

Conclusions: The intricate web of crosstalk among the often redundant multitudes of signaling intermediates is just beginning to be understood. Future research employing genome-scale systems biology approaches to solve problems of such magnitude will undoubtedly lead to a better understanding of plant development. Therefore, discovering additional crosstalk mechanisms among various hormones in coordinating growth under stress will be an important theme in the field of abiotic stress research. Such efforts will help to reveal important points of genetic control that can be useful to engineer stress tolerant crops.
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http://dx.doi.org/10.1186/s12870-016-0771-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831116PMC
April 2016

Data in support of the proteomic analysis of plasma membrane and tonoplast from the leaves of mangrove plant Avicennia officinalis.

Data Brief 2015 Dec 26;5:646-52. Epub 2015 Oct 26.

Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore ; NUS Environmental Research Institute (NERI), National University of Singapore, Singapore.

The data provides information in support of the research article, Proteomics 2014, 14, 2545-2557 [1]. Raw data is available from the ProteomeXchange Consortium via the PRIDE partnerRepository [2] with the dataset identifier PXD000837. Plasma membrane and tonoplast proteins from the leaves of Avicennia officinalis were identified using gel electrophoresis (one and two dimensional) combined with LC-MS analysis. Based on GO annotation, identified proteins were predicted to be involved in various biological processes.
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http://dx.doi.org/10.1016/j.dib.2015.10.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644245PMC
December 2015

Salt tolerance research in date palm tree (Phoenix dactylifera L.), past, present, and future perspectives.

Front Plant Sci 2015 18;6:348. Epub 2015 May 18.

Department of Biological Sciences, National University of Singapore , Singapore, Singapore.

The date palm can adapt to extreme drought, to heat, and to relatively high levels of soil salinity. However, excessive amounts of salt due to irrigation with brackish water lead to a significant reduction in the productivity of the fruits as well as marked decrease in the viable numbers of the date palm trees. It is imperative that the nature of the existing salt-adaptation mechanism be understood in order to develop future date palm varieties that can tolerate excessive soil salinity. In this perspective article, several research strategies, obstacles, and precautions are discussed in light of recent advancements accomplished in this field and the properties of this species. In addition to a physiological characterization, we propose the use of a full range of OMICS technologies, coupled with reverse genetics approaches, aimed toward understanding the salt-adaption mechanism in the date palm. Information generated by these analyses should highlight transcriptional and posttranscriptional modifications controlling the salt-adaptation mechanisms. As an extremophile with a natural tolerance for a wide range of abiotic stresses, the date palm may represent a treasure trove of novel genetic resources for salinity tolerance.
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http://dx.doi.org/10.3389/fpls.2015.00348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4434913PMC
June 2015

Destabilization of interaction between cytokinin signaling intermediates AHP1 and ARR4 modulates Arabidopsis development.

New Phytol 2015 Apr 30;206(2):726-37. Epub 2015 Jan 30.

Department of Biological Sciences, Faculty of Science, National University of Singapore, 117543, Singapore, Singapore.

Eukaryotic two-component signaling involves the His-Asp-His-Asp multistep phosphorelay (MSP). In Arabidopsis thaliana, cytokinin-mediated MSP signaling intermediates include histidine kinases (HKs), histidine phosphotransfer proteins (Hpts) and response regulators (RRs). The structure-function relationship of interaction between Hpt (e.g. AHP1) and RR (e.g. ARR4) is poorly understood. Using a homology model and yeast two-hybrid analysis, we identified key amino acids of ARR4 at the AHP1-ΔARR4((16-175)) interaction interface. Mutating them in Arabidopsis (arr3,4,5,6,8,9 hextuple mutant background) and performing root length assays provided functional relevance, and coimmunoprecipitation (coIP) assay provided biochemical evidence for the interaction. The homology model mimics crystal structures of Hpt-RR complexes. Mutating selected interface residues of ARR4 either abolished or destabilized the interaction. D45A and Y96A mutations weakened interaction with AHP1, and exhibited weaker rescue of root elongation in the hextuple mutants. CoIP analysis using cytokinin-treated transgenic Arabidopsis seedlings provided biochemical evidence for weakened AHP1-ARR4 interaction. The relevance of the selected residues for the interaction was further validated in two independent pairs of Hpt-RR proteins from Arabidopsis and rice (Oryza sativa). Our data provide evidence of a link between Hpt-RR interaction affinity and regulation of downstream functions of RRs. This establishes a structure-function relationship for the final step of a eukaryotic MSP signal cascade.
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http://dx.doi.org/10.1111/nph.13297DOI Listing
April 2015

A hormone-responsive C1-domain-containing protein At5g17960 mediates stress response in Arabidopsis thaliana.

PLoS One 2015 15;10(1):e0115418. Epub 2015 Jan 15.

Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore; Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore.

Phytohormones play a critical role in mediating plant stress response. They employ a variety of proteins for coordinating such processes. In Arabidopsis thaliana, some members of a Cys-rich protein family known as C1-clan proteins were involved in stress response, but the actual function of the protein family is largely unknown. We studied At5g17960, a C1-clan protein member that possesses three unique C1 signature domains viz. C1_2, C1_3 and ZZ/PHD type. Additionally, we identified 72 other proteins in A. thaliana that contain all three unique signature domains. Subsequently, the 73 proteins were phylogenetically classified into IX subgroups. Promoter motif analysis of the 73 genes identified the presence of hormone-responsive and stress-responsive putative cis-regulatory elements. Furthermore, we observed that transcript levels of At5g17960 were induced in response to different hormones and stress treatments. At1g35610 and At3g13760, two other members of subgroup IV, also showed upregulation upon GA3, biotic and abiotic stress treatments. Moreover, seedlings of independent transgenic A. thaliana lines ectopically expressing or suppressing At5g17960 also showed differential regulation of several abiotic stress-responsive marker genes. Thus, our data suggest that C1-domain-containing proteins have a role to play in plant hormone-mediated stress responses, thereby assigning a putative function for the C1-clan protein family.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115418PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4295845PMC
December 2015

Identification of salt gland-associated genes and characterization of a dehydrin from the salt secretor mangrove Avicennia officinalis.

BMC Plant Biol 2014 Nov 18;14:291. Epub 2014 Nov 18.

Background: Salt stress is a major challenge for growth and development of plants. The mangrove tree Avicennia officinalis has evolved salt tolerance mechanisms such as salt secretion through specialized glands on its leaves. Although a number of structural studies on salt glands have been done, the molecular mechanism of salt secretion is not clearly understood. Also, studies to identify salt gland-specific genes in mangroves have been scarce.

Results: By subtractive hybridization (SH) of cDNA from salt gland-rich cell layers (tester) with mesophyll tissues as the driver, several Expressed Sequence Tags (ESTs) were identified. The major classes of ESTs identified include those known to be involved in regulating metabolic processes (37%), stress response (17%), transcription (17%), signal transduction (17%) and transport functions (12%). A visual interactive map generated based on predicted functional gene interactions of the identified ESTs suggested altered activities of hydrolase, transmembrane transport and kinases. Quantitative Real-Time PCR (qRT-PCR) was carried out to validate the expression specificity of the ESTs identified by SH. A Dehydrin gene was chosen for further experimental analysis, because it is significantly highly expressed in salt gland cells, and dehydrins are known to be involved in stress remediation in other plants. Full-length Avicennia officinalis Dehydrin1 (AoDHN1) cDNA was obtained by Rapid Amplification of cDNA Ends. Phylogenetic analysis and further characterization of this gene suggested that AoDHN1 belongs to group II Late Embryogenesis Abundant proteins. qRT-PCR analysis of Avicennia showed up-regulation of AoDHN1 in response to salt and drought treatments. Furthermore, some functional insights were obtained by growing E. coli cells expressing AoDHN1. Growth of E. coli cells expressing AoDHN1 was significantly higher than that of the control cells without AoDHN1 under salinity and drought stresses, suggesting that the mangrove dehydrin protein helps to mitigate the abiotic stresses.

Conclusions: Thirty-four ESTs were identified to be enriched in salt gland-rich tissues of A. officinalis leaves. qRT-PCR analysis showed that 10 of these were specifically enriched in the salt gland-rich tissues. Our data suggest that one of the selected genes, namely, AoDHN1 plays an important role to mitigate salt and drought stress responses.
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http://dx.doi.org/10.1186/s12870-014-0291-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247641PMC
November 2014

Proteomic analysis of plasma membrane and tonoplast from the leaves of mangrove plant Avicennia officinalis.

Proteomics 2014 Nov;14(21-22):2545-57

Department of Biological Sciences, National University of Singapore, Singapore; NUS Environmental Research Institute (NERI), National University of Singapore, Singapore.

In order to understand the salt tolerance and secretion in mangrove plant species, gel electrophoresis coupled with LC-MS-based proteomics was used to identify key transport proteins in the plasma membrane (PM) and tonoplast fractions of Avicennia officinalis leaves. PM and tonoplast proteins were purified using two-aqueous-phase partitioning and density gradient centrifugation, respectively. Forty of the 254 PM proteins and 31 of the 165 tonoplast proteins identified were predicted to have transmembrane domains. About 95% of the identified proteins could be classified based on their functions. The major classes of proteins were predicted to be involved in transport, metabolic processes, defense/stress response, and signal transduction, while a few of the proteins were predicted to be involved in other functions such as membrane trafficking. The main classes of transporter proteins identified included H(+) -ATPases, ATP-binding cassette transporters, and aquaporins, all of which could play a role in salt secretion. These data will serve as the baseline membrane proteomic dataset for Avicennia species. Further, this information can contribute to future studies on understanding the mechanism of salt tolerance in halophytes in addition to salt secretion in mangroves. All MS data have been deposited in the ProteomeXchange with identifier PXD000837 (http://proteomecentral.proteomexchange.org/dataset/PXD000837).
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http://dx.doi.org/10.1002/pmic.201300527DOI Listing
November 2014

TIR1-like auxin-receptors are involved in the regulation of plum fruit development.

J Exp Bot 2014 Oct 4;65(18):5205-15. Epub 2014 Jul 4.

University of Guelph, Department of Plant Agriculture. 4890 Victoria Av. N., P.O. Box 7000 Vineland Station, ON, L0R 2E0 Canada

Ethylene has long been considered the key regulator of ripening in climacteric fruit. Recent evidence showed that auxin also plays an important role during fruit ripening, but the nature of the interaction between the two hormones has remained unclear. To understand the differences in ethylene- and auxin-related behaviours that might reveal how the two hormones interact, we compared two plum (Prunus salicina L.) cultivars with widely varying fruit development and ripening ontogeny. The early-ripening cultivar, Early Golden (EG), exhibited high endogenous auxin levels and auxin hypersensitivity during fruit development, while the late-ripening cultivar, V98041 (V9), displayed reduced auxin content and sensitivity. We show that exogenous auxin is capable of dramatically accelerating fruit development and ripening in plum, indicating that this hormone is actively involved in the ripening process. Further, we demonstrate that the variations in auxin sensitivity between plum cultivars could be partially due to PslAFB5, which encodes a TIR1-like auxin receptor. Two different PslAFB5 alleles were identified, one (Pslafb5) inactive due to substitution of the conserved F-box amino acid residue Pro61 to Ser. The early-ripening cultivar, EG, exhibited homozygosity for the inactive allele; however, the late cultivar, V9, displayed a PslAFB5/afb5 heterozygous genotype. Our results highlight the impact of auxin in stimulating fruit development, especially the ripening process and the potential for differential auxin sensitivity to alter important fruit developmental processes.
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http://dx.doi.org/10.1093/jxb/eru279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157706PMC
October 2014

Role of root hydrophobic barriers in salt exclusion of a mangrove plant Avicennia officinalis.

Plant Cell Environ 2014 Jul 19;37(7):1656-71. Epub 2014 Feb 19.

Department of Biological Sciences, National University of Singapore, 117543, Singapore; NUS Environmental Research Institute (NERI), National University of Singapore, 117411, Singapore.

Salt exclusion at the roots and salt secretion in the leaves were examined in a mangrove, Avicennia officinalis. The non-secretor mangrove Bruguiera cylindrica was used for comparative study of hydrophobic barrier formation in the roots. Bypass flow was reduced when seedlings were previously treated with high salt concentration. A biseriate exodermis was detected in the salt-treated roots, along with an enhanced deposition of hydrophobic barriers in the endodermis. These barriers reduced Na(+) loading into the xylem, accounting for a 90-95% salt exclusion in A. officinalis. Prominent barriers were found in the roots of B. cylindrica even in the absence of salt treatment. A cytochrome P450 gene that may regulate suberin biosynthesis was up-regulated within hours of salt treatment in A. officinalis roots and leaves, corresponding with increased suberin deposition. X-ray microanalysis showed preferential deposition of Na(+) and Cl(-) in the root cortex compared with the stele, suggesting that the endodermis is the primary site of salt exclusion. Enhanced salt secretion and increased suberin deposition surrounding the salt glands were seen in the leaves with salt treatment. Overall, these data show that the deposition of apoplastic barriers increases resistance to bypass flow leading to efficient salt exclusion at the roots in mangroves.
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http://dx.doi.org/10.1111/pce.12272DOI Listing
July 2014

Characterization of gibberellin-signalling elements during plum fruit ontogeny defines the essentiality of gibberellin in fruit development.

Plant Mol Biol 2014 Mar 20;84(4-5):399-413. Epub 2013 Oct 20.

Department of Plant Agriculture, University of Guelph, 4890 Victoria Av. N., P.O. Box 7000, Vineland Station, ON, L0R 2E0, Canada.

Fruit growth is a coordinated, complex interaction of cell division, differentiation and expansion. Gibberellin (GA) involvement in the reproductive events is an important aspect of GA effects. Perennial fruit-trees such as plum (Prunus salicina L.) have distinct features that are economically important and provide opportunities to dissect specific GA mechanisms. Currently, very little is known on the molecular mechanism(s) mediating GA effects on fruit development. Determination of bioactive GA content during plum fruit ontogeny revealed that GA1 and GA4 are critical for fruit growth and development. Further, characterization of several genes involved in GA-signalling showed that their transcriptional regulation are generally GA-dependent, confirming their involvement in GA-signalling. Based on these results, a model is presented elucidating how the potential association between GA and other hormones may contribute to fruit development. PslGID1 proteins structure, Y2H and BiFC assays indicated that plum GA-receptors can form a complex with AtDELLA-repressors in a GA-dependent manner. Moreover, phenotypical-, molecular- and GA-analyses of various Arabidopsis backgrounds ectopically expressing PslGID1 sequences provide evidence on their role as active GA-signalling components that mediate GA-responsiveness. Our findings support the critical contribution of GA alone or in association with other hormones in mediating plum fruit growth and development.
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http://dx.doi.org/10.1007/s11103-013-0139-8DOI Listing
March 2014

Identification and characterization of RcMADS1, an AGL24 ortholog from the holoparasitic plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae).

PLoS One 2013 28;8(6):e67243. Epub 2013 Jun 28.

Department of Biological Sciences, Faculty of Science, National University of Singapore, Republic of Singapore.

Rafflesia, a holoparasitic genus that produces the largest flower in the world is characterized by the absence of leaves, stem and other macroscopic organs. To better understand the molecular regulation of flower development in this genus we isolated and characterized a floral MADS-box gene, namely, RcMADS1 from Rafflesia cantleyi. Heterologous expression analysis in Arabidopsis was chosen because Rafflesia is not amenable to genetic manipulations. RcMADS1 shares sequence similarity with AGAMOUS-LIKE 24 (AGL24) and SHORT VEGETATIVE PHASE (SVP) of Arabidopsis. Ectopic expression of RcMADS1 in Arabidopsis caused early flowering and conversion of sepals and petals into leaf-like structures, and carpels into inflorescences. In 35S::RcMADS1 plants SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), a downstream target gene of AGL24, was upregulated. 35S::RcMADS1 plants exhibit early flowering and conversion of the floral meristem into inflorescence meristem, as in 35S::AGL24 plants. Similar to AGL24, RcMADS1 could rescue the late flowering phenotypes of agl24-1 and FRIGIDA, but not the early flowering of svp-41. Based on these results, we propose that RcMADS1 is a functional ortholog of Arabidopsis AGL24.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067243PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695966PMC
January 2014

The phytohormone crosstalk paradigm takes center stage in understanding how plants respond to abiotic stresses.

Plant Cell Rep 2013 Jul 8;32(7):945-57. Epub 2013 Jun 8.

Genetics and Biotechnology Division, Plant Breeding, International Rice Research Institute, 7777 Manila, Philippines.

The highly coordinated, dynamic nature of growth requires plants to perceive and react to various environmental signals in an interactive manner. Elaborate signaling networks mediate this plasticity in growth and the ability to adapt to changing environmental conditions. The fluctuations of stress-responsive hormones help alter the cellular dynamics and hence play a central role in coordinately regulating the growth responses under stress. Recent experimental data unequivocally demonstrated that interactions among various phytohormones are the rule rather than exception in integrating the diverse input signals and readjusting growth as well as acquiring stress tolerance. The presence of multiple and often redundant signaling intermediates for each phytohormone appears to help in such crosstalk. Furthermore, there are several examples of similar developmental changes occurring in response to distinct abiotic stress signals, which can be explained by the crosstalk in phytohormone signaling. Therefore, in this brief review, we have highlighted the major phytohormone crosstalks with a focus on the response of plants to abiotic stresses. The recent findings have made it increasingly apparent that such crosstalk will also explain the extreme pleiotropic responses elicited by various phytohormones. Indeed, it would not be presumptuous to expect that in the coming years this paradigm will take a central role in explaining developmental regulation.
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http://dx.doi.org/10.1007/s00299-013-1461-yDOI Listing
July 2013

Regulation of biotic and abiotic stress responses by plant hormones.

Authors:
Prakash P Kumar

Plant Cell Rep 2013 Jul 29;32(7):943. Epub 2013 May 29.

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http://dx.doi.org/10.1007/s00299-013-1460-zDOI Listing
July 2013
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