1
|
Zimran G, Feuer E, Pri-Tal O, Shpilman M, Mosquna A. Directed Evolution of Herbicide Biosensors in a Fluorescence-Activated Cell-Sorting-Compatible Yeast Two-Hybrid Platform. ACS Synth Biol 2022; 11:2880-2888. [PMID: 35922400 PMCID: PMC9396700 DOI: 10.1021/acssynbio.2c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
![]()
Developing sensory modules for specific molecules of
interest represents
a fundamental challenge in synthetic biology and its applications.
A somewhat generalizable approach for this challenge is demonstrated
here by evolving a naturally occurring chemically induced heterodimer
into a genetically encoded sensor for herbicides. The interaction
between PYRABACTIN-RESISTANT-like receptors and type-2C protein phosphatases
is induced by abscisic acid—a small-molecule hormone in plants.
We considered abscisic acid receptors as a potential scaffold for
the development of biosensors because of past successes in their engineering,
a structurally defined ligand cavity and the availability of large-scale
assays for their activation. A panel of 475 receptor variants, mutated
at ligand-proximal residues, was screened for activation by 37 herbicides
from several classes. Twelve compounds activated at least one member
of the mutant panel. To facilitate the subsequent improvement of herbicide
receptors through directed evolution, we engineered a yeast two-hybrid
platform optimized for sequential positive and negative selection
using fluorescence-activated cell sorting. By utilizing this system,
we were able to isolate receptors with low nanomolar sensitivity and
a broad dynamic range in sensing a ubiquitous group of chloroacetamide
herbicides. Aside from its possible applicative value, this work lays
down conceptual groundwork and provides infrastructure for the future
development of biosensors through directed evolution.
Collapse
Affiliation(s)
- Gil Zimran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Erez Feuer
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Oded Pri-Tal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Michal Shpilman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| |
Collapse
|
2
|
Feuer E, Zimran G, Shpilman M, Mosquna A. A Modified Yeast Two-Hybrid Platform Enables Dynamic Control of Expression Intensities to Unmask Properties of Protein-Protein Interactions. ACS Synth Biol 2022; 11:2589-2598. [PMID: 35895499 PMCID: PMC9442787 DOI: 10.1021/acssynbio.2c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The yeast two-hybrid (Y2H) assay is widely used for protein-protein interaction characterization due to its simplicity and accessibility. However, it may mask changes in affinity caused by mutations or ligand activation due to signal saturation. To overcome this drawback, we modified the Y2H system to have tunable protein expression by introducing a fluorescent reporter and a pair of synthetic inducible transcription factors to regulate the expression of interacting components. We found that the application of inducers allowed us to adjust the concentrations of interacting proteins to avoid saturation and observe interactions otherwise masked in the canonical Y2H assay, such as the abscisic acid-mediated increase in affinity of monomeric abscisic acid receptors to the coreceptor. When applied in future studies, our modified system may provide a more accurate characterization of protein-protein interactions.
Collapse
Affiliation(s)
- Erez Feuer
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Gil Zimran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Michal Shpilman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| |
Collapse
|
3
|
Mao H, Jian C, Cheng X, Chen B, Mei F, Li F, Zhang Y, Li S, Du L, Li T, Hao C, Wang X, Zhang X, Kang Z. The wheat ABA receptor gene TaPYL1-1B contributes to drought tolerance and grain yield by increasing water-use efficiency. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:846-861. [PMID: 34890091 PMCID: PMC9055818 DOI: 10.1111/pbi.13764] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/28/2021] [Accepted: 12/03/2021] [Indexed: 05/14/2023]
Abstract
The role of abscisic acid (ABA) receptors, PYR1/PYL/RCAR (PYLs), is well established in ABA signalling and plant drought response, but limited research has explored the regulation of wheat PYLs in this process, especially the effects of their allelic variations on drought tolerance or grain yield. Here, we found that the overexpression of a TaABFs-regulated PYL gene, TaPYL1-1B, exhibited higher ABA sensitivity, photosynthetic capacity and water-use efficiency (WUE), all contributed to higher drought tolerance than that of wild-type plants. This heightened water-saving mechanism further increased grain yield and protected productivity during water deficit. Candidate gene association analysis revealed that a favourable allele TaPYL1-1BIn-442 , carrying an MYB recognition site insertion in the promoter, is targeted by TaMYB70 and confers enhanced expression of TaPYL1-1B in drought-tolerant genotypes. More importantly, an increase in frequency of the TaPYL1-1BIn-442 allele over decades among modern Chinese cultivars and its association with high thousand-kernel weight together demonstrated that it was artificially selected during wheat improvement efforts. Taken together, our findings illuminate the role of TaPYL1-1B plays in coordinating drought tolerance and grain yield. In particular, the allelic variant TaPYL1-1BIn-442 substantially contributes to enhanced drought tolerance while maintaining high yield, and thus represents a valuable genetic target for engineering drought-tolerant wheat germplasm.
Collapse
Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Chao Jian
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Xinxiu Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Bin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Yifang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Shumin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life ScienceNorthwest A&F UniversityYanglingShaanxi712100China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Xiaojing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life ScienceNorthwest A&F UniversityYanglingShaanxi712100China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
- Yangling Seed Industry Innovation CenterYanglingShaanxi712100China
| |
Collapse
|
4
|
Pizzio GA, Mayordomo C, Lozano-Juste J, Garcia-Carpintero V, Vazquez-Vilar M, Nebauer SG, Kaminski KP, Ivanov NV, Estevez JC, Rivera-Moreno M, Albert A, Orzaez D, Rodriguez PL. PYL1- and PYL8-like ABA Receptors of Nicotiana benthamiana Play a Key Role in ABA Response in Seed and Vegetative Tissue. Cells 2022; 11:795. [PMID: 35269417 PMCID: PMC8909036 DOI: 10.3390/cells11050795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 02/04/2023] Open
Abstract
To face the challenges of climate change and sustainable food production, it is essential to develop crop genome editing techniques to pinpoint key genes involved in abiotic stress signaling. The identification of those prevailing abscisic acid (ABA) receptors that mediate plant-environment interactions is quite challenging in polyploid plants because of the high number of genes in the PYR/PYL/RCAR ABA receptor family. Nicotiana benthamiana is a biotechnological crop amenable to genome editing, and given the importance of ABA signaling in coping with drought stress, we initiated the analysis of its 23-member family of ABA receptors through multiplex CRISPR/Cas9-mediated editing. We generated several high-order mutants impaired in NbPYL1-like and NbPYL8-like receptors, which showed certain insensitivity to ABA for inhibition of seedling establishment, growth, and development of shoot and lateral roots as well as reduced sensitivity to the PYL1-agonist cyanabactin (CB). However, in these high-order mutants, regulation of transpiration was not affected and was responsive to ABA treatment. This reveals a robust and redundant control of transpiration in this allotetraploid plant that probably reflects its origin from the extreme habitat of central Australia.
Collapse
Affiliation(s)
- Gaston A. Pizzio
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Cristian Mayordomo
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Victor Garcia-Carpintero
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Sergio G. Nebauer
- Plant Production Department, Universitat Politècnica de València, ES-46022 Valencia, Spain;
| | - Kacper P. Kaminski
- PMI R&D, Philip Morris Products S.A., Quai Jean Renaud 5, CH-2000 Neuchâtel, Switzerland; (K.P.K.); (N.V.I.)
| | - Nikolai V. Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jean Renaud 5, CH-2000 Neuchâtel, Switzerland; (K.P.K.); (N.V.I.)
| | - Juan C. Estevez
- Centro Singular de Investigación en Química e Bioloxía Molecular (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Maria Rivera-Moreno
- Instituto de Química-Física Rocasolano, Departamento de Cristalografía y Biología Estructural, CSIC, ES-28006 Madrid, Spain; (M.R.-M.); (A.A.)
| | - Armando Albert
- Instituto de Química-Física Rocasolano, Departamento de Cristalografía y Biología Estructural, CSIC, ES-28006 Madrid, Spain; (M.R.-M.); (A.A.)
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| | - Pedro L. Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain; (G.A.P.); (C.M.); (J.L.-J.); (V.G.-C.); (M.V.-V.); (D.O.)
| |
Collapse
|
5
|
Wang J, Xu Y, Zhang W, Zheng Y, Yuan B, Li Q, Leng P. Tomato SlPP2C5 Is Involved in the Regulation of Fruit Development and Ripening. PLANT & CELL PHYSIOLOGY 2021; 62:1760-1769. [PMID: 34428298 DOI: 10.1093/pcp/pcab130] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/06/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Abscisic acid (ABA) regulates plant development mainly through its signaling, in which ABA binds to receptors to inhibit type 2C protein phosphatases (PP2Cs). The exact roles of PP2Cs in fruit development are still unclear. In this work, we verify that tomato SlPP2C5 works as a negative regulator in ABA signaling during fruit development. SlPP2C5 was inhibited by both monomeric and dimeric ABA receptors SlPYLs through ABA dose-dependent way, and it interacted physically with SlPYLs and SlSnRK2s. SlPP2C5 was highly expressed in fruits induced by exogenous ABA. Plants with overexpressed SlPP2C5 had lower sensitivity to ABA, which showed faster seed germination and primary root growth compared to Wild type (WT), while SlPP2C5-suppressed plants were more sensitive to ABA. SlPP2C5-over-expression (OE) delayed fruit ripening onset, while SlPP2C5-RNAi advanced fruit ripening. Alteration of SlPP2C5 expression impacts fruit quality parameters as well, including pericarp thickness, fruit shape index, seed number and weight and the soluble solid content. RNA-seq analysis revealed that there were significant expression differences of genes related to ethylene release and lycopene synthesis between WT and both SlPP2C5-OE and SlPP2C5-RNAi lines with an inversed variation. Taken together, our findings demonstrate that SlPP2C5 plays an important role in the regulation of fruit development, ripening and quality.
Collapse
Affiliation(s)
- Juan Wang
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Yandan Xu
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Wenbo Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Yu Zheng
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Bing Yuan
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Qian Li
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Ping Leng
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| |
Collapse
|
6
|
Yu L, Ma S, Zhang X, Tian D, Yang S, Jia X, Traw MB. Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1365-1381. [PMID: 34585814 DOI: 10.1111/tpj.15516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/03/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Whole genome duplication (WGD) in plants is typically followed by genomic downsizing, where large portions of the new genome are lost. Whether this downsizing is accompanied by increased or decreased evolutionary rates of the remaining genes is poorly known, not least because homeolog pairings are often obscured by chromosomal rearrangement. Here, we use the newly published genome from a sedge, namely Kobresia littledalei, and CRISPR/Cas-9 editing to investigate how the Rho WGD event 70 million years ago (MYA) affected transcription factor evolutionary rates, fates, and function in rice (Oryza sativa) and sorghum (Sorghum bicolor). We focus on the 30-member DNA-binding with one zinc finger (Dof) transcription factor family in both crops due to their agronomic importance. Using the known speciation dates of rice from Kobresia (97 MYA) and sorghum (50 MYA), we find that rates of amino acid substitution in the critical Dof domain region were over twofold higher during the 20-million-year period following the WGD than before or afterward. Through comparison of synteny blocks, we report that at least 11% of Dof genes were purged from 70 to 50 MYA, while only 6% have been lost in the most recent 50-million-year interval. CRISPR/Cas9 editing revealed widespread fitness-related defects in flowering and lack of redundancy of paired members, as well as significant differences in expression between gene pairs. Together these findings demonstrate the strength of Dof genes as a model for deep evolutionary study and offer one of the most detailed portraits yet of the Rho WGD impact on a gene lineage.
Collapse
Affiliation(s)
- Luyao Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shiying Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xianqing Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Key Laboratory of Plant Nutrition and Fertilizers, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Milton Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| |
Collapse
|
7
|
Ruiz-Partida R, Rosario SM, Lozano-Juste J. An Update on Crop ABA Receptors. PLANTS 2021; 10:plants10061087. [PMID: 34071543 PMCID: PMC8229007 DOI: 10.3390/plants10061087] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/06/2021] [Accepted: 05/13/2021] [Indexed: 11/19/2022]
Abstract
The hormone abscisic acid (ABA) orchestrates the plant stress response and regulates sophisticated metabolic and physiological mechanisms essential for survival in a changing environment. Plant ABA receptors were described more than 10 years ago, and a considerable amount of information is available for the model plant Arabidopsis thaliana. Unfortunately, this knowledge is still very limited in crops that hold the key to feeding a growing population. In this review, we summarize genomic, genetic and structural data obtained in crop ABA receptors. We also provide an update on ABA perception in major food crops, highlighting specific and common features of crop ABA receptors.
Collapse
Affiliation(s)
- Rafael Ruiz-Partida
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Calle Ingeniero Fausto Elio s/n, Edificio 8E, 46022 Valencia, Spain; (R.R.-P.); (S.M.R.)
| | - Sttefany M. Rosario
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Calle Ingeniero Fausto Elio s/n, Edificio 8E, 46022 Valencia, Spain; (R.R.-P.); (S.M.R.)
- Laboratorio de Biología Molecular, Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo (UASD), Camino de Engombe, Santo Domingo 10904, Dominican Republic
| | - Jorge Lozano-Juste
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Calle Ingeniero Fausto Elio s/n, Edificio 8E, 46022 Valencia, Spain; (R.R.-P.); (S.M.R.)
- Correspondence:
| |
Collapse
|
8
|
Yadav SK, Santosh Kumar VV, Verma RK, Yadav P, Saroha A, Wankhede DP, Chaudhary B, Chinnusamy V. Genome-wide identification and characterization of ABA receptor PYL gene family in rice. BMC Genomics 2020; 21:676. [PMID: 32998689 PMCID: PMC7526420 DOI: 10.1186/s12864-020-07083-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/18/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Abscisic acid (ABA), a key phytohormone that controls plant growth and stress responses, is sensed by the pyrabactin resistance 1(PYR1)/PYR1-like (PYL)/regulatory components of the ABA receptor (RCAR) family of proteins. Comprehensive information on evolution and function of PYL gene family in rice (Oryza sativa) needs further investigation. This study made detailed analysis on evolutionary relationship between PYL family members, collinearity, synteny, gene structure, protein motifs, cis-regulatory elements (CREs), SNP variations, miRNAs targeting PYLs and expression profiles in different tissues and stress responses. RESULTS Based on sequence homology with Arabidopsis PYL proteins, we identified a total of 13 PYLs in rice (BOP clade) and maize (PACCMAD clade), while other members of BOP (wheat - each diploid genome, barley and Brachypodium) and PACCMAD (sorghum and foxtail millet) have 8-9 PYLs. The phylogenetic analysis divided PYLs into three subfamilies that are structurally and functionally conserved across species. Gene structure and motif analysis of OsPYLs revealed that members of each subfamily have similar gene and motif structure. Segmental duplication appears be the driving force for the expansion of PYLs, and the majority of the PYLs underwent evolution under purifying selection in rice. 32 unique potential miRNAs that might target PYLs were identified in rice. Thus, the predicted regulation of PYLs through miRNAs in rice is more elaborate as compared with B. napus. Further, the miRNAs identified to in this study were also regulated by stresses, which adds additional layer of regulation of PYLs. The frequency of SAPs identified was higher in indica cultivars and were predominantly located in START domain that participate in ABA binding. The promoters of most of the OsPYLs have cis-regulatory elements involved in imparting abiotic stress responsive expression. In silico and q-RT-PCR expression analyses of PYL genes revealed multifaceted role of ABARs in shaping plant development as well as abiotic stress responses. CONCLUSION The predicted miRNA mediated regulation of OsPYLs and stress regulated expression of all OsPYLs, at least, under one stress, lays foundation for further validation and fine tuning ABA receptors for stress tolerance without yield penalty in rice.
Collapse
Affiliation(s)
- Shashank Kumar Yadav
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.,School of Biotechnology, Gautam Buddha University, Greater Noida, UP, 201310, India
| | | | - Rakesh Kumar Verma
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Pragya Yadav
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Ankit Saroha
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | | | - Bhupendra Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida, UP, 201310, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.
| |
Collapse
|
9
|
Effects of Exogenous Abscisic Acid (ABA) on Carotenoids and Petal Color in Osmanthus fragrans 'Yanhonggui'. PLANTS 2020; 9:plants9040454. [PMID: 32260328 PMCID: PMC7238031 DOI: 10.3390/plants9040454] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/16/2023]
Abstract
Osmanthus fragrans is a well-known native plant in China, and carotenoids are the main group of pigments in the petals. Abscisic acid (ABA) is one of the products of the metabolic pathway of carotenoids. Application of ABA could affect pigmentation of flower petals by changing the carotenoid content. However, little is known about the effects of ABA treatment on carotenoid accumulation in O. fragrans. In this study, different concentrations of ABA (0, 150 and 200 mg/L) were spread on the petals of O. fragrans 'Yanhonggui'. The petal color of 'Yanhonggui' receiving every ABA treatment was deeper than that of the control. The content of total carotenoids in the petals significantly increased with 200 mg/L ABA treatment. In the petals, α-carotene and β-carotene were the predominant carotenoids. The expression of several genes involved in the metabolism of carotenoids increased with 200 mg/L ABA treatment, including PSY1, PDS1, Z-ISO1, ZDS1, CRTISO, NCED3 and CCD4. However, the transcription levels of the latter two carotenoid degradation-related genes were much lower than of the five former carotenoid biosynthesis-related genes; the finding would explain the significant increase in total carotenoids in 'Yanhonggui' petals receiving the 200 mg/L ABA treatment.
Collapse
|
10
|
Li H, Gao Z, Chen Q, Li Q, Luo M, Wang J, Hu L, Zahid MS, Wang L, Zhao L, Song S, Xu W, Zhang C, Ma C, Wang S. Grapevine ABA receptor VvPYL1 regulates root hair development in Transgenic Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 149:190-200. [PMID: 32078897 DOI: 10.1016/j.plaphy.2020.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 06/10/2023]
Abstract
Root architecture is very important for plant growth. In this study, we characterized the process of root formation in grapevine (Vitis vinifera L.). Continuous observation of root morphology during development revealed that the establishment of root system could be divided into five stages: initial cultivation (stage I), preliminary development (stage II), even change (stage III), root system formation (stage IV), and root architecture stability (stage V). The level of abscisic acid (ABA) increased from stages II to IV and was stable at stage V. Quantitative expression analysis of 11 genes encoding ABA-related rate-limiting enzymes in different tissues showed that the expression of VvPYL1 was the highest in roots. Spatiotemporal expression analysis showed that VvPYL1 was highly expressed during stages II and III. Furthermore, VvPYL1 was highly expressed in lateral roots of grapevine seedlings in tissue culture. Overexpression of VvPYL1 in Arabidopsis thaliana resulted in longer root hairs compared with wild-type plants. Moreover, the root hair length of transgenic lines was hypersensitive to exogenously applied ABA. Additionally, VvPYL1 overexpressing plants showed greater drought tolerance and longer root hairs than wild-type plants under osmotic stress. These results suggest that VvPYL1 may play a key role in root development and drought resistance.
Collapse
Affiliation(s)
- Hui Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhen Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Qiuju Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qin Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Luo
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Liping Hu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Salman Zahid
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Liping Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shiren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China; Institute of Agro-food Science and Technology, Key Laboratory of Agro-products Processing Technology of Shandong, Shandong Academy of Agricultural Sciences, Jinan, China.
| |
Collapse
|
11
|
Sun Y, Pri-Tal O, Michaeli D, Mosquna A. Evolution of Abscisic Acid Signaling Module and Its Perception. FRONTIERS IN PLANT SCIENCE 2020; 11:934. [PMID: 32754170 PMCID: PMC7367143 DOI: 10.3389/fpls.2020.00934] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/08/2020] [Indexed: 05/18/2023]
Abstract
We hereby review the perception and responses to the stress hormone Abscisic acid (ABA), along the trajectory of 500M years of plant evolution, whose understanding may resolve how plants acquired this signaling pathway essential for the colonization of land. ABA levels rise in response to abiotic stresses, coordinating physiological and metabolic responses, helping plants survive stressful environments. In land plants, ABA signaling cascade leads to growth arrest and large-scale changes in transcript levels, required for coping with environmental stressors. This response is regulated by a PYRABACTIN RESISTANCE 1-like (PYL)-PROTEIN PHOSPHATASE 2C (PP2C)-SNF1-RELATED PROTEIN KINASE 2 (SnRK2) module, that initiates phosphor-activation of transcription factors and ion channels. The enzymatic portions of this module (phosphatase and kinase) are functionally conserved from streptophyte algae to angiosperms, whereas the regulatory component -the PYL receptors, putatively evolved in the common ancestor of Zygnematophyceae and embryophyte as a constitutive, ABA-independent protein, further evolving into a ligand-activated receptor at the embryophyta. This evolutionary process peaked with the appearance of the strictly ABA-dependent subfamily III stress-triggered angiosperms' dimeric PYL receptors. The emerging picture is that the ancestor of land plants and its predecessors synthesized ABA, as its biosynthetic pathway is conserved between ancestral and current day algae. Despite this ability, it was only the common ancestor of land plants which acquired the hormonal-modulation of PYL activity by ABA. This raises several questions regarding both ABA's function in ABA-non-responsive organisms, and the evolutionary aspects of the ABA signal transduction pathway.
Collapse
Affiliation(s)
- Yufei Sun
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Oded Pri-Tal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- *Correspondence: Assaf Mosquna,
| |
Collapse
|
12
|
Kai W, Wang J, Liang B, Fu Y, Zheng Y, Zhang W, Li Q, Leng P. PYL9 is involved in the regulation of ABA signaling during tomato fruit ripening. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6305-6319. [PMID: 31504753 PMCID: PMC6859720 DOI: 10.1093/jxb/erz396] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 08/21/2019] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA) regulates fruit ripening, yet little is known about the exact roles of ABA receptors in fruit. In this study, we reveal the role of SlPYL9, a tomato pyrabactin resistance (PYR)/pyrobactin resistance-like (PYL)/regulatory component of ABA receptors (RCAR) protein, as a positive regulator of ABA signaling and fruit ripening. SlPYL9 inhibits protein phosphatase-type 2C (PP2C2/6) in an ABA dose-dependent way, and it interacts physically with SlPP2C2/3/4/5 in an ABA-dependent manner. Expression of SlPYL9 was observed in the seeds, flowers, and fruits. Overexpression and suppression of SlPYL9 induced a variety of phenotypes via altered expression of ABA signaling genes (SlPP2C1/2/9, SlSnRK2.8, SlABF2), thereby affecting expression of ripening-related genes involved in ethylene release and cell wall modification. SlPYL9-OE/RNAi plants showed a typical ABA hyper-/hypo-sensitive phenotype in terms of seed germination, primary root growth, and response to drought. Fruit ripening was significantly accelerated in SlPYL9-OE by 5-7 d as a result of increased endogenous ABA accumulation and advanced release of ethylene compared with the wild-type. In the SlPYL9-RNAi lines, fruit ripening was delayed, mesocarp thickness was enhanced, and petal abscission was delayed compared with the wild-type, resulting in conical/oblong and gourd-shaped fruits. These results suggest that SlPYL9 is involved in ABA signaling, thereby playing a role in the regulation of flower abscission and fruit ripening in tomato.
Collapse
Affiliation(s)
- Wenbin Kai
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Juan Wang
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Bin Liang
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Ying Fu
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Yu Zheng
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Wenbo Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | | | | |
Collapse
|
13
|
Papacek M, Christmann A, Grill E. Increased water use efficiency and water productivity of arabidopsis by abscisic acid receptors from Populus canescens. ANNALS OF BOTANY 2019; 124:581-590. [PMID: 30629104 PMCID: PMC6821255 DOI: 10.1093/aob/mcy225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 12/06/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Water deficit is the single most important factor limiting plant productivity in the field. Poplar is a crop used for second-generation bioenergy production that can be cultivated on marginal land without competing for land use in food production. Poplar has a high demand for water, which makes improving its water use efficiency (WUE) an attractive goal. Recently, we showed that enhanced expression of specific receptors of arabidopsis for the phytohormone abscisic acid (ABA) can improve WUE in arabidopsis and water productivity, i.e. more biomass is formed per unit of water over time. In this study, we examined whether ABA receptors from poplar can enhance WUE and water productivity in arabidopsis. METHODS ABA receptors from poplar were stably introduced into arabidopsis for analysis of their effect on water use efficiency. Physiological analysis included growth assessment and gas exchange measurements. KEY RESULTS The data presented here are in agreement with the functionality of poplar ABA receptors in arabidopsis, which led to ABA-hypersensitive seed germination and root growth. In addition, arabidopsis lines expressing poplar RCAR10, but not RCAR9, showed increased WUE by up to 26 % compared with the wild type with few trade-offs in growth that also resulted in higher water productivity during drought. The improved WUE was mediated by reduced stomatal conductance, a steeper CO2 gradient at the leaf boundary and sustained photosynthesis resulting in an increased intrinsic WUE (iWUE). CONCLUSIONS The analysis is a case study supporting the use of poplar ABA receptors for improving WUE and showing the feasibility of using a heterologous expression strategy for generating plants with improved water productivity.
Collapse
Affiliation(s)
- Michael Papacek
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße, Freising, Germany
| | - Alexander Christmann
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße, Freising, Germany
| | - Erwin Grill
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße, Freising, Germany
- For correspondence. E-mail
| |
Collapse
|
14
|
Li X, Wu L, Qiu Y, Wang T, Zhou Q, Zhang Q, Zhang W, Liu Z. Abscisic Acid Receptors Modulate Metabolite Levels and Phenotype in Arabidopsis Under Normal Growing Conditions. Metabolites 2019; 9:metabo9110249. [PMID: 31652982 PMCID: PMC6918416 DOI: 10.3390/metabo9110249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 01/01/2023] Open
Abstract
Abscisic acid (ABA) is a vital phytohormone that accumulates in response to various biotic and abiotic stresses, as well as plant growth. In Arabidopsis thaliana, there are 14 members of the ABA receptor family, which are key positive regulators involved in ABA signaling. Besides reduced drought stress tolerance, the quadruple and sextuple mutants (pyr1pyl1pyl2pyl4 (1124) and pyr1pyl1pyl2pyl4pyl5pyl8 (112458) show abnormal growth phenotypes, such as decreases in yield and height, under non-stress conditions. However, it remains unknown whether ABA receptors mediate ABA signaling to regulate plant growth and development. Here, we showed the primary metabolite profiles of 1124, 112458 and wild-type (WT) plants grown under normal conditions. The metabolic changes were significantly different between ABA receptor mutants and WT. Guanosine, for the biosynthesis of cyclic guanosine 3′,5′-monophosphate (cGMP), is an important second messenger that acts to regulate the level of ABA. In addition, other amino acids were increased in the 112458 mutant, including proline. These results, together with phenotype analysis, indicated that ABA receptors are involved in ABA signaling to modulate metabolism and plant growth under normal conditions.
Collapse
Affiliation(s)
- Xiaoyi Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Lintao Wu
- Rape Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China.
| | - Yao Qiu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Tao Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Qin Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Qian Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Wei Zhang
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong 643000, China.
| | - Zhibin Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| |
Collapse
|
15
|
Lozano-Juste J, Masi M, Cimmino A, Clement S, Fernández MA, Antoni R, Meyer S, Rodriguez PL, Evidente A. The fungal sesquiterpenoid pyrenophoric acid B uses the plant ABA biosynthetic pathway to inhibit seed germination. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5487-5494. [PMID: 31257433 PMCID: PMC6793445 DOI: 10.1093/jxb/erz306] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/17/2019] [Indexed: 05/12/2023]
Abstract
Pyrenophoric acid (P-Acid), P-Acid B, and P-Acid C are three phytotoxic sesquiterpenoids produced by the ascomycete seed pathogen Pyrenophora semeniperda, a fungus proposed as a mycoherbicide for biocontrol of cheatgrass, an extremely invasive weed. When tested in cheatgrass bioassays, these metabolites were able to delay seed germination, with P-Acid B being the most active compound. Here, we have investigated the cross-kingdom activity of P-Acid B and its mode of action, and found that it activates the abscisic acid (ABA) signaling pathway in order to inhibit seedling establishment. P-Acid B inhibits seedling establishment in wild-type Arabidopsis thaliana, while several mutants affected in the early perception as well as in downstream ABA signaling components were insensitive to the fungal compound. However, in spite of structural similarities between ABA and P-Acid B, the latter is not able to activate the PYR/PYL family of ABA receptors. Instead, we have found that P-Acid B uses the ABA biosynthesis pathway at the level of alcohol dehydrogenase ABA2 to reduce seedling establishment. We propose that the fungus P. semeniperda manipulates plant ABA biosynthesis as a strategy to reduce seed germination, increasing its ability to cause seed mortality and thereby increase its fitness through higher reproductive success.
Collapse
Affiliation(s)
- Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
- Correspondence: or
| | - Marco Masi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo, Napoli, Italy
| | - Alessio Cimmino
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo, Napoli, Italy
| | - Suzette Clement
- Shrub Sciences Laboratory, U.S. Forest Service Rocky Mountain Research Station, Provo, UT, USA
| | - Maria A Fernández
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Regina Antoni
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Susan Meyer
- Shrub Sciences Laboratory, U.S. Forest Service Rocky Mountain Research Station, Provo, UT, USA
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Antonio Evidente
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo, Napoli, Italy
- Correspondence: or
| |
Collapse
|
16
|
Dittrich M, Mueller HM, Bauer H, Peirats-Llobet M, Rodriguez PL, Geilfus CM, Carpentier SC, Al Rasheid KAS, Kollist H, Merilo E, Herrmann J, Müller T, Ache P, Hetherington AM, Hedrich R. The role of Arabidopsis ABA receptors from the PYR/PYL/RCAR family in stomatal acclimation and closure signal integration. NATURE PLANTS 2019; 5:1002-1011. [PMID: 31451795 DOI: 10.1038/s41477-019-0490-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 07/09/2019] [Indexed: 05/26/2023]
Abstract
Stomata are microscopic pores found on the surfaces of leaves that act to control CO2 uptake and water loss. By integrating information derived from endogenous signals with cues from the surrounding environment, the guard cells, which surround the pore, 'set' the stomatal aperture to suit the prevailing conditions. Much research has concentrated on understanding the rapid intracellular changes that result in immediate changes to the stomatal aperture. In this study, we look instead at how stomata acclimate to longer timescale variations in their environment. We show that the closure-inducing signals abscisic acid (ABA), increased CO2, decreased relative air humidity and darkness each access a unique gene network made up of clusters (or modules) of common cellular processes. However, within these networks some gene clusters are shared amongst all four stimuli. All stimuli modulate the expression of members of the PYR/PYL/RCAR family of ABA receptors. However, they are modulated differentially in a stimulus-specific manner. Of the six members of the PYR/PYL/RCAR family expressed in guard cells, PYL2 is sufficient for guard cell ABA-induced responses, whereas in the responses to CO2, PYL4 and PYL5 are essential. Overall, our work shows the importance of ABA as a central regulator and integrator of long-term changes in stomatal behaviour, including sensitivity, elicited by external signals. Understanding this architecture may aid in breeding crops with improved water and nutrient efficiency.
Collapse
Affiliation(s)
- Marcus Dittrich
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Heike M Mueller
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| | - Hubert Bauer
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| | - Marta Peirats-Llobet
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, Valencia, Spain
- Centre for AgriBioscience, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria, Australia
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, Valencia, Spain
| | - Christoph-Martin Geilfus
- Division of Controlled Environment Horticulture, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-University of Berlin, Berlin, Germany
| | - Sebastien Christian Carpentier
- SYBIOMA, Proteomics Core Facility, KU Leuven, Leuven, Belgium
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | | | - Hannes Kollist
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ebe Merilo
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Johannes Herrmann
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany.
| | - Peter Ache
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| | | | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| |
Collapse
|
17
|
Dittrich M, Mueller HM, Bauer H, Peirats-Llobet M, Rodriguez PL, Geilfus CM, Carpentier SC, Al Rasheid KAS, Kollist H, Merilo E, Herrmann J, Müller T, Ache P, Hetherington AM, Hedrich R. The role of Arabidopsis ABA receptors from the PYR/PYL/RCAR family in stomatal acclimation and closure signal integration. NATURE PLANTS 2019; 5:1002-1011. [PMID: 31451795 DOI: 10.1038/s41477-019-0490-490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 07/09/2019] [Indexed: 05/22/2023]
Abstract
Stomata are microscopic pores found on the surfaces of leaves that act to control CO2 uptake and water loss. By integrating information derived from endogenous signals with cues from the surrounding environment, the guard cells, which surround the pore, 'set' the stomatal aperture to suit the prevailing conditions. Much research has concentrated on understanding the rapid intracellular changes that result in immediate changes to the stomatal aperture. In this study, we look instead at how stomata acclimate to longer timescale variations in their environment. We show that the closure-inducing signals abscisic acid (ABA), increased CO2, decreased relative air humidity and darkness each access a unique gene network made up of clusters (or modules) of common cellular processes. However, within these networks some gene clusters are shared amongst all four stimuli. All stimuli modulate the expression of members of the PYR/PYL/RCAR family of ABA receptors. However, they are modulated differentially in a stimulus-specific manner. Of the six members of the PYR/PYL/RCAR family expressed in guard cells, PYL2 is sufficient for guard cell ABA-induced responses, whereas in the responses to CO2, PYL4 and PYL5 are essential. Overall, our work shows the importance of ABA as a central regulator and integrator of long-term changes in stomatal behaviour, including sensitivity, elicited by external signals. Understanding this architecture may aid in breeding crops with improved water and nutrient efficiency.
Collapse
Affiliation(s)
- Marcus Dittrich
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Heike M Mueller
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| | - Hubert Bauer
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| | - Marta Peirats-Llobet
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, Valencia, Spain
- Centre for AgriBioscience, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria, Australia
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, Valencia, Spain
| | - Christoph-Martin Geilfus
- Division of Controlled Environment Horticulture, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-University of Berlin, Berlin, Germany
| | - Sebastien Christian Carpentier
- SYBIOMA, Proteomics Core Facility, KU Leuven, Leuven, Belgium
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | | | - Hannes Kollist
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ebe Merilo
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Johannes Herrmann
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany.
| | - Peter Ache
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| | | | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| |
Collapse
|
18
|
Bai G, Xie H, Yao H, Li F, Chen X, Zhang Y, Xiao B, Yang J, Li Y, Yang DH. Genome-wide identification and characterization of ABA receptor PYL/RCAR gene family reveals evolution and roles in drought stress in Nicotiana tabacum. BMC Genomics 2019; 20:575. [PMID: 31296158 PMCID: PMC6625023 DOI: 10.1186/s12864-019-5839-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Abscisic acid (ABA) is an important phytohormone for plant growth, development and responding to stresses such as drought, salinity, and pathogen infection. Pyrabactin Resistance 1 (PYR1)/PYR1-Like (PYL)/Regulatory Component of ABA Receptor (RCAR) (hereafter referred to as PYLs) has been identified as the ABA receptors. The PYL family members have been well studied in many plants. However, the members of PYL family have not been systematically identified at genome level in cultivated tobacco (Nicotiana tabacum) and its two ancestors. In this study, the phylogenic relationships, chromosomal distribution, gene structures, conserved motifs/regions, and expression profiles of NtPYLs were analyzed. RESULTS We identified 29, 11, 16 PYLs in the genomes of allotetraploid N. tabacum, and its two diploid ancestors N. tomentosiformis and N. sylvestris, respectively. The phylogenetic analysis revealed that NtPYLs can be divided into three subfamilies, and each NtPYL has one counterpart in N. sylvestris or N. tomentosiformis. Based on microarray analysis of NtPYL transcripts, four NtPYLs (from subfamily II, III), and five NtPYLs (from subfamily I) are highlighted as potential candidates for further functional characterization in N. tabacum seed development, response to ABA, and germination, and resistance to abiotic stresses, respectively. Interestingly, the expression profiles of members in the same NtPYL subfamily showed somehow similar patterns in tissues at different developmental stages and in leaves of seedlings under drought stress, suggesting particular NtPYLs might have multiple functions in both plant development and drought stress response. CONCLUSIONS NtPYLs are highlighted for important functions in seed development, germination and response to ABA, and particular in drought tolerance. This work will not only shed light on the PYL family in tobacco, but also provides some valuable information for functional characterization of ABA receptors in N. tabacum.
Collapse
Affiliation(s)
- Ge Bai
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan China
| | - He Xie
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan China
| | - Heng Yao
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan China
| | - Feng Li
- National Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, Henan China
| | - Xuejun Chen
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan China
| | - Yihan Zhang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan China
| | - Bingguan Xiao
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan China
| | - Jun Yang
- National Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, Henan China
| | - Yongping Li
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan China
| | - Da-Hai Yang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan China
| |
Collapse
|
19
|
Yoshida T, Christmann A, Yamaguchi-Shinozaki K, Grill E, Fernie AR. Revisiting the Basal Role of ABA - Roles Outside of Stress. TRENDS IN PLANT SCIENCE 2019; 24:625-635. [PMID: 31153771 DOI: 10.1016/j.tplants.2019.04.008] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/23/2019] [Accepted: 04/26/2019] [Indexed: 05/04/2023]
Abstract
The physiological roles of abscisic acid (ABA) as a stress hormone in plant responses to water shortage, including stomatal regulation and gene expression, have been well documented. However, less attention has been paid to the function of basal ABA synthesized under well-watered conditions in recent studies. In this review, we summarize progress in the understanding of how low concentrations of ABA are perceived at the molecular level and how its signaling affects plant metabolism and growth under nonstressed conditions. We also discuss the dual nature of ABA in acting as an inhibitor and activator of plant growth and development.
Collapse
Affiliation(s)
- Takuya Yoshida
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany.
| | - Alexander Christmann
- Lehrstuhl für Botanik, Technische Universität München, D-85354 Freising, Germany
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 113-8657 Tokyo, Japan
| | - Erwin Grill
- Lehrstuhl für Botanik, Technische Universität München, D-85354 Freising, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| |
Collapse
|
20
|
Sterlin Y, Pri-Tal O, Zimran G, Park SY, Ben-Ari J, Kourelis J, Verstraeten I, Gal M, Cutler SR, Mosquna A. Optimized small-molecule pull-downs define MLBP1 as an acyl-lipid-binding protein. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:928-941. [PMID: 30735592 DOI: 10.1111/tpj.14272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/02/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Abscisic acid (ABA) receptors belong to the START domain superfamily, which encompasses ligand-binding proteins present in all kingdoms of life. START domain proteins contain a central binding pocket that, depending on the protein, can couple ligand binding to catalytic, transport or signaling functions. In Arabidopsis, the best characterized START domain proteins are the 14 PYR/PYL/RCAR ABA receptors, while the other members of the superfamily do not have assigned ligands. To address this, we used affinity purification of biotinylated proteins expressed transiently in Nicotiana benthamiana coupled to untargeted LC-MS to identify candidate binding ligands. We optimized this method using ABA-PYL interactions and show that ABA co-purifies with wild-type PYL5 but not a binding site mutant. The Kd of PYL5 for ABA is 1.1 μm, which suggests that the method has sufficient sensitivity for many ligand-protein interactions. Using this method, we surveyed a set of 37 START domain-related proteins, which resulted in the identification of ligands that co-purified with MLBP1 (At4G01883) or MLP165 (At1G35260). Metabolite identification and the use of authentic standards revealed that MLBP1 binds to monolinolenin, which we confirmed using recombinant MLBP1. Monolinolenin also co-purified with MLBP1 purified from transgenic Arabidopsis, demonstrating that the interaction occurs in a native context. Thus, deployment of this relatively simple method allowed us to define a protein-metabolite interaction and better understand protein-ligand interactions in plants.
Collapse
Affiliation(s)
- Yelena Sterlin
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Oded Pri-Tal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Gil Zimran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Sang-Youl Park
- Department of Botany and Plant Sciences, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Julius Ben-Ari
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Jiorgos Kourelis
- Department of Botany and Plant Sciences, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Inge Verstraeten
- Department of Botany and Plant Sciences, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Maayan Gal
- Biochemistry Department, MIGAL-Galilee Research Institute, Kiryat-Shmona , 11016, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, 1220800, Israel
| | - Sean R Cutler
- Department of Botany and Plant Sciences, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| |
Collapse
|
21
|
Wiseglass G, Pri-Tal O, Mosquna A. ABA signaling components in Phelipanche aegyptiaca. Sci Rep 2019; 9:6476. [PMID: 31019234 PMCID: PMC6482195 DOI: 10.1038/s41598-019-42976-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/12/2019] [Indexed: 11/09/2022] Open
Abstract
Obligate root holoparasite Phelipanche aegyptiaca is an agricultural pest, which infests its hosts and feeds on the sap, subsequently damaging crop yield and quality. Its notoriously viable seed bank may serve as an ideal pest control target. The phytohormone abscisic acid (ABA) was shown to regulate P. aegyptiaca seed dormancy following strigolactones germination stimulus. Transcription analysis of signaling components revealed five ABA receptors and two co-receptors (PP2C). Transcription of lower ABA-affinity subfamily III receptors was absent in all tested stages of P. aegyptiaca development and parasitism stages. P. aegyptiaca ABA receptors interacted with the PP2Cs, and inhibited their activity in an ABA-dependent manner. Moreover, sequence analysis revealed multiple alleles in two P. aegyptiaca ABA receptors, with many non-synonymous mutations. Functional analysis of selected receptor alleles identified a variant with substantially decreased inhibitory effect of PP2Cs activity in-vitro. These results provide evidence that P. aegyptiaca is capable of biochemically perceiving ABA. In light of the possible involvement of ABA in parasitic activities, the discovery of active ABA receptors and PP2Cs could provide a new biochemical target for the agricultural management of P. aegyptiaca. Furthermore, the potential genetic loss of subfamily III receptors in this species, could position P. aegyptiaca as a valuable model in the ABA perception research field.
Collapse
Affiliation(s)
- Gil Wiseglass
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Oded Pri-Tal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| |
Collapse
|
22
|
Ectopic expression of mutated type 2C protein phosphatase OsABI-LIKE2 decreases abscisic acid sensitivity in Arabidopsis and rice. Sci Rep 2018; 8:12320. [PMID: 30120350 PMCID: PMC6097999 DOI: 10.1038/s41598-018-30866-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 08/06/2018] [Indexed: 12/02/2022] Open
Abstract
Abscisic acid (ABA) is a phytohormone that is necessary for stress adaptation. Recent studies have reported that attenuated levels of ABA improved grain yield and seedling growth under low temperature in cereals. To improve plant growth under low temperature, we attempted to generate ABA-insensitive transgenic rice by expressing a clade A type 2C protein phosphatase (OsPP2C), OsABIL2, with or without the mutation equivalent to the Arabidopsis abi1-1 mutation. A yeast two-hybrid assay revealed that the interaction between OsABIL2 and a putative rice ABA receptor, OsPYL1, was ABA-dependent, and the interaction was lost with amino acid substitution from glycine to aspartic acid at the 183rd amino acid of the OsABIL2 protein, corresponding to abi1-1 mutation. The constitutive expression of OsABIL2 or OsABIL2G183D in Arabidopsis or rice decreased ABA sensitivity to differing degrees. Moreover, the transgenic rice expressing OsABIL2G183D exhibited improved seedling growth under low temperature, although the transgenic lines showed unfavorable traits, such as viviparous germination and elongated internodes. These results indicated that the introduction of abi1-1 type dominant mutation was also effective in OsABIL2 at decreasing ABA sensitivity in plants, and the attenuation of ABA sensitivity could be an alternative parameter to improve rice performance under low temperatures.
Collapse
|
23
|
Dejonghe W, Okamoto M, Cutler SR. Small Molecule Probes of ABA Biosynthesis and Signaling. PLANT & CELL PHYSIOLOGY 2018; 59:1490-1499. [PMID: 29986078 DOI: 10.1093/pcp/pcy126] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/26/2018] [Indexed: 05/07/2023]
Abstract
The phytohormone ABA mediates many physiological and developmental responses, and its key role in plant water relations has fueled efforts to improve crop water productivity by manipulating ABA responses. ABA's core signaling components are encoded by large gene families, which has hampered functional studies using classical genetic approaches due to redundancy. Chemical approaches can complement genetic approaches and have the advantage of delivering both biological probes and potential agrochemical leads; these benefits have spawned the discovery and design of new chemical modulators of ABA signaling and biosynthesis, which have contributed to the identification of ABA receptors and helped to define PYR1 and related subfamily III receptors as key cellular targets for chemically manipulating water productivity. In this review, we provide an overview of small molecules that have helped dissect both ABA signaling and metabolic pathways. We further discuss how the insights gleaned using ABA probe molecules might be translated to improvements in crop water productivity and future opportunities for development of small molecules that affect ABA metabolism and signaling.
Collapse
Affiliation(s)
- Wim Dejonghe
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Masanori Okamoto
- Center for Bioscience Research and Education, Utsunomiya University, 350 Mine-cho, Utsunomiya, Tochigi, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Sean R Cutler
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| |
Collapse
|
24
|
He Z, Zhong J, Sun X, Wang B, Terzaghi W, Dai M. The Maize ABA Receptors ZmPYL8, 9, and 12 Facilitate Plant Drought Resistance. FRONTIERS IN PLANT SCIENCE 2018; 9:422. [PMID: 29670640 PMCID: PMC5893742 DOI: 10.3389/fpls.2018.00422] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 03/16/2018] [Indexed: 05/04/2023]
Abstract
Drought is one of the major abiotic stresses affecting world agriculture. Breeding drought-resistant crops is one of the most important challenges for plant biologists. PYR1/PYL/RCARs, which encode the abscisic acid (ABA) receptors, play pivotal roles in ABA signaling, but how these genes function in crop drought response remains largely unknown. Here we identified 13 PYL family members in maize (ZmPYL1-13). Changes in expression of these genes under different stresses indicated that ZmPYLs played important roles in responding to multiple abiotic stresses. Transgenic analyses of ZmPYL genes in Arabidopsis showed that overexpression of ZmPYL3, ZmPYL9, ZmPYL10, and ZmPYL13 significantly enhanced the sensitivity of transgenic plants to ABA. Additionally, transgenic lines overexpressing ZmPYL8, ZmPYL9, and ZmPYL12 were more resistant to drought. Accumulation of proline and enhanced expression of drought-related marker genes in transgenic lines further confirmed the positive roles of ZmPYL genes in plant drought resistance. Association analyses with a panel of 368 maize inbred lines identified natural variants in ZmPYL8 and ZmPYL12 that were significantly associated with maize drought resistance. Our results deepen the knowledge of the function of maize PYL genes in responses to abiotic stresses, and the natural variants identified in ZmPYL genes may serve as potential molecular markers for breeding drought-resistant maize cultivars.
Collapse
Affiliation(s)
- Zhenghua He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Junwei Zhong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaopeng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Bingcai Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, PA, United States
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
25
|
Tannenbaum M, Sarusi-Portuguez A, Krispil R, Schwartz M, Loza O, Benichou JIC, Mosquna A, Hakim O. Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq. PLANT METHODS 2018; 14:113. [PMID: 30598689 PMCID: PMC6300899 DOI: 10.1186/s13007-018-0381-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/10/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors (TFs) to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus, the accessibility of these loci for TF binding is highly regulated and determines where and when TFs bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana and define organ-specific regulatory sites and binding motifs of TFs at these sites. RESULTS We coupled the recently described isolation of nuclei tagged in specific cell types (INTACT) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions but are correlated with root-specific expression of distant genes. Importantly, these gene-distant sites are enriched for binding motifs of TFs important for root development as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel gene-distant regulatory elements. CONCLUSIONS By coupling INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root-specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.
Collapse
Affiliation(s)
- Miriam Tannenbaum
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Avital Sarusi-Portuguez
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Ronen Krispil
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Michal Schwartz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Olga Loza
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Jennifer I. C. Benichou
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Assaf Mosquna
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| |
Collapse
|
26
|
Vaidya AS, Peterson FC, Yarmolinsky D, Merilo E, Verstraeten I, Park SY, Elzinga D, Kaundal A, Helander J, Lozano-Juste J, Otani M, Wu K, Jensen DR, Kollist H, Volkman BF, Cutler SR. A Rationally Designed Agonist Defines Subfamily IIIA Abscisic Acid Receptors As Critical Targets for Manipulating Transpiration. ACS Chem Biol 2017; 12:2842-2848. [PMID: 28949512 DOI: 10.1021/acschembio.7b00650] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing drought and diminishing freshwater supplies have stimulated interest in developing small molecules that can be used to control transpiration. Receptors for the plant hormone abscisic acid (ABA) have emerged as key targets for this application, because ABA controls the apertures of stomata, which in turn regulate transpiration. Here, we describe the rational design of cyanabactin, an ABA receptor agonist that preferentially activates Pyrabactin Resistance 1 (PYR1) with low nanomolar potency. A 1.63 Å X-ray crystallographic structure of cyanabactin in complex with PYR1 illustrates that cyanabactin's arylnitrile mimics ABA's cyclohexenone oxygen and engages the tryptophan lock, a key component required to stabilize activated receptors. Further, its sulfonamide and 4-methylbenzyl substructures mimic ABA's carboxylate and C6 methyl groups, respectively. Isothermal titration calorimetry measurements show that cyanabactin's compact structure provides ready access to high ligand efficiency on a relatively simple scaffold. Cyanabactin treatments reduce Arabidopsis whole-plant stomatal conductance and activate multiple ABA responses, demonstrating that its in vitro potency translates to ABA-like activity in vivo. Genetic analyses show that the effects of cyanabactin, and the previously identified agonist quinabactin, can be abolished by the genetic removal of PYR1 and PYL1, which form subclade A within the dimeric subfamily III receptors. Thus, cyanabactin is a potent and selective agonist with a wide spectrum of ABA-like activities that defines subfamily IIIA receptors as key target sites for manipulating transpiration.
Collapse
Affiliation(s)
- Aditya S. Vaidya
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Francis C. Peterson
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Dmitry Yarmolinsky
- Institute
of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Ebe Merilo
- Institute
of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | | | - Sang-Youl Park
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Dezi Elzinga
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Amita Kaundal
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Jonathan Helander
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | | | - Masato Otani
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Kevin Wu
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Davin R. Jensen
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Hannes Kollist
- Institute
of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Brian F. Volkman
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Sean R. Cutler
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| |
Collapse
|