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Ahmad R, Ullah I, Ullah Z, Alam S, Rady A, Khan SS, Durrani IS. Genomic Exploration: Unraveling the Intricacies of Indica Rice Oryza sativa L. Germin-Like Protein Gene 12-3 ( OsGLP12-3) Promoter via Cloning, Sequencing, and In Silico Analysis. ACS OMEGA 2024; 9:15271-15281. [PMID: 38585130 PMCID: PMC10993326 DOI: 10.1021/acsomega.3c09670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/21/2024] [Accepted: 03/05/2024] [Indexed: 04/09/2024]
Abstract
Germin and Germin-like proteins (GLPs) are a class of plant proteins that are part of the Cupins superfamily, found in several plant organs including roots, seeds, leaves, and nectar glands. They play a crucial role in plant defense against pathogens and environmental stresses. Herein, this study focused on the promoter analysis of OsGLP12-3 in rice cultivar Swat-1 to elucidate its regulation and functions. The region (1863bp) of the OsGLP12-3 promoter from Swat-1 genomic DNA was amplified, purified, quantified, and cloned using Topo cloning technology, followed by sequencing. Further in silico comparative analysis was conducted between the OsGLP12-3 promoters from Nipponbare and Swat-1 using the Plant CARE database, identifying 24 cis-acting regulatory elements with diverse functions. These elements exhibited distinct distribution patterns in the 2 rice varieties. The OsGLP12-3 promoter revealed an abundance of regulatory elements associated with biotic and abiotic stress responses. Computational tools were employed to analyze the regulatory features of this region. In silico expression analysis of OsGLP12-3, considering various developmental stages, stress conditions, hormones, and expression timing, was performed using the TENOR tool. Pairwise alignment indicated 86% sequence similarity between Nipponbare and Swat-1. Phylogenetic analysis was conducted to explore the evolutionary relationship between the OsGLP12-3 and other plant GLPs. Additionally, 2 unique regulatory elements were modeled and docked, GARE and MBS to understand their hydrogen bonding interactions in gene regulation. The study highlights the importance of OsGLP12-3 in plant defense against biotic and abiotic stresses, supported by its expression patterns in response to various stressors and the presence of specific regulatory elements within its promoter region.
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Affiliation(s)
- Rashid Ahmad
- Institute
of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Irfan Ullah
- College
of Life Science and Technology, Beijing
University of Chemical Technology, Beijing 100029, China
| | - Zakir Ullah
- College
of Life Science and Technology, Beijing
University of Chemical Technology, Beijing 100029, China
| | - Shahab Alam
- Institute
of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Ahmed Rady
- Department
of Zoology, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shahin Shah Khan
- College
of Life Science and Technology, Beijing
University of Chemical Technology, Beijing 100029, China
| | - Irfan Safdar Durrani
- Institute
of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
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Gao Z, Zhou Y, He Y. Molecular epigenetic mechanisms for the memory of temperature stresses in plants. J Genet Genomics 2022; 49:991-1001. [PMID: 35870761 DOI: 10.1016/j.jgg.2022.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 12/29/2022]
Abstract
The sessile plants encounter various stresses; some are prolonged, whereas some others are recurrent. Temperature is crucial for plant growth and development, and plants often encounter adverse high temperature fluctuations (heat stresses) as well as prolonged cold exposure such as seasonal temperature drops in winter when grown in temperate regions. Many plants can remember past temperature stresses to get adapted to adverse local temperature changes to ensure survival and/or reproductive success. Here, we summarize chromatin-based mechanisms underlying acquired thermotolerance or thermomemory in plants and review recent progresses on molecular epigenetic understanding of 'remembering of prolonged cold in winter' or vernalization, a process critical for various over-wintering plants to acquire competence to flower in the coming spring. In addition, perspectives on future study in temperature stress memories of economically-important crops are discussed.
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Affiliation(s)
- Zhaoxu Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuehui He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China.
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3
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Chen S, Hou J, Fu Y, Li H. Genome-wide identification of YABBY transcription factors in Brachypodium distachyon and functional characterization of Bd DROOPING LEAF. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 185:13-24. [PMID: 35640497 DOI: 10.1016/j.plaphy.2022.05.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/17/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
YABBY transcription factors (TFs) are plant-specific and are characterized by a C2-C2 zinc finger domain at the N-terminus and a YABBY domain at the C-terminus. In this study, eight YABBY genes were identified in the Brachypodium distachyon genome and were unevenly distributed across four chromosomes. Phylogenetic analysis classified BdYABBYs into FIL/YAB3, YAB2, CRC, and INO clades. Sixty-two putative cis-elements were identified in BdYABBY gene putative promoters, among them, CAAT-box, TATA-box, MYB, MYC, ARE, and Box_4 were shared by all. BdYABBY genes are highly expressed in inflorescences, and abiotic stresses regulate their expression. In addition, three transcripts of BdDL were identified. Over-expression in Arabidopsis has shown their different functions in reproductive development, as well as in response to cold stress. Our study lays the foundation for the functional elucidation of BdYABBY genes.
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Affiliation(s)
- Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000, Shaanxi, China.
| | - Jiayuan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000, Shaanxi, China.
| | - Yanan Fu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000, Shaanxi, China.
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000, Shaanxi, China.
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Nibau C, van de Koot W, Spiliotis D, Williams K, Kramaric T, Beckmann M, Mur L, Hiwatashi Y, Doonan JH. Molecular and physiological responses to desiccation indicate the abscisic acid pathway is conserved in the peat moss, Sphagnum. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4576-4591. [PMID: 35383351 PMCID: PMC9291362 DOI: 10.1093/jxb/erac133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Mosses of the genus Sphagnum are the main components of peatlands, a major carbon-storing ecosystem. Changes in precipitation patterns are predicted to affect water relations in this ecosystem, but the effect of desiccation on the physiological and molecular processes in Sphagnum is still largely unexplored. Here we show that different Sphagnum species have differential physiological and molecular responses to desiccation but, surprisingly, this is not directly correlated with their position in relation to the water table. In addition, the expression of drought responsive genes is increased upon water withdrawal in all species. This increase in gene expression is accompanied by an increase in abscisic acid (ABA), supporting a role for ABA during desiccation responses in Sphagnum. Not only do ABA levels increase upon desiccation, but Sphagnum plants pre-treated with ABA display increased tolerance to desiccation, suggesting that ABA levels play a functional role in the response. In addition, many of the ABA signalling components are present in Sphagnum and we demonstrate, by complementation in Physcomitrium patens, that Sphagnum ABI3 is functionally conserved. The data presented here, therefore, support a conserved role for ABA in desiccation responses in Sphagnum.
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Affiliation(s)
| | - Willem van de Koot
- National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Dominic Spiliotis
- National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Kevin Williams
- National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Tina Kramaric
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Manfred Beckmann
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Luis Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Yuji Hiwatashi
- School of Food Industrial Sciences, Miyagi University, Sendai, Japan
| | - John H Doonan
- National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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Ding LN, Liu R, Li T, Li M, Liu XY, Wang WJ, Yu YK, Cao J, Tan XL. Physiological and comparative transcriptome analyses reveal the mechanisms underlying waterlogging tolerance in a rapeseed anthocyanin-more mutant. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:55. [PMID: 35596185 PMCID: PMC9123723 DOI: 10.1186/s13068-022-02155-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/11/2022] [Indexed: 12/13/2022]
Abstract
Background Rapeseed (Brassica napus) is the second largest oil crop worldwide. It is widely used in food, energy production and the chemical industry, as well as being an ornamental. Consequently, it has a large economic value and developmental potential. Waterlogging is an important abiotic stress that restricts plant growth and development. However, little is known about the molecular mechanisms underlying waterlogging tolerance in B. napus. Results In the present study, the physiological changes and transcriptomes of germination-stage rapeseed in response to waterlogging stress were investigated in the B. napus cultivar ‘Zhongshuang 11’ (ZS11) and its anthocyanin-more (am) mutant, which was identified in our previous study. The mutant showed stronger waterlogging tolerance compared with ZS11, and waterlogging stress significantly increased anthocyanin, soluble sugar and malondialdehyde contents and decreased chlorophyll contents in the mutant after 12 days of waterlogging. An RNA-seq analysis identified 1370 and 2336 differently expressed genes (DEGs) responding to waterlogging stress in ZS11 and am, respectively. An enrichment analysis revealed that the DEGs in ZS11 were predominately involved in carbohydrate metabolism, whereas those in the am mutant were particularly enriched in plant hormone signal transduction and response to endogenous stimulation. In total, 299 DEGs were identified as anthocyanin biosynthesis-related structural genes (24) and regulatory genes encoding transcription factors (275), which may explain the increased anthocyanin content in the am mutant. A total of 110 genes clustered in the plant hormone signal transduction pathway were also identified as DEGs, including 70 involved in auxin and ethylene signal transduction that were significantly changed in the mutant. Furthermore, the expression levels of 16 DEGs with putative roles in anthocyanin accumulation and biotic/abiotic stress responses were validated by quantitative real-time PCR as being consistent with the transcriptome profiles. Conclusion This study provides new insights into the molecular mechanisms of increased anthocyanin contents in rapeseed in response to waterlogging stress, which should be useful for reducing the damage caused by waterlogging stress and for further breeding new rapeseed varieties with high waterlogging tolerance. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02155-5.
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Affiliation(s)
- Li-Na Ding
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Rui Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Teng Li
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ming Li
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiao-Yan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Wei-Jie Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yan-Kun Yu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang, China.
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Lee SE, Yoon IS, Hwang YS. Abscisic acid activation of oleosin gene HvOle3 expression prevents the coalescence of protein storage vacuoles in barley aleurone cells. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:817-834. [PMID: 34698829 DOI: 10.1093/jxb/erab471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Protein storage vacuoles (PSVs) in aleurone cells coalesce during germination, and this process is highly coupled with mobilization of PSV reserves, allowing de novo synthesis of various hydrolases in aleurone cells for endosperm degradation. Here we show that in barley (Hordeum vulgare L.) oleosins, the major integral proteins of oleosomes are encoded by four genes (HvOle1 to 4), and the expression of HvOle1 and HvOle3 is strongly up-regulated by abscisic acid (ABA), which shows antagonism to gibberellic acid. In aleurone cells, all HvOLEs were subcellularly targeted to the tonoplast of PSVs. Gain-of-function analyses revealed that HvOLE3 effectively delayed PSV coalescence, whereas HvOLE1 only had a moderate effect, with no notable effect of HvOLE2 and 4. With regard to longevity, HvOLE3 chiefly outperformed other HvOLEs, followed by HvOLE1. Experiments swapping the N- and C-terminal domain between HvOLE3 and other HvOLEs showed that the N-terminal region of HvOLE3 is mainly responsible, with some positive effect by the C-terminal region, for mediating the specific preventive effect of HvOLE3 on PSV coalescence. Three ACGT-core elements and the RY-motif were responsible for ABA induction of HvOle3 promoter activity. Transient expression assays using aleurone protoplasts demonstrated that transcriptional activation of the HvOle3 promoter was mediated by transcription factors HvABI3 and HvABI5, which acted downstream of protein kinase HvPKABA1.
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Affiliation(s)
- Sung-Eun Lee
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - In Sun Yoon
- Gene Engineering Division, National Institute of Agricultural Sciences, Jeonju 565-851, Republic of Korea
| | - Yong-Sic Hwang
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
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7
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Guillory A, Bonhomme S. Phytohormone biosynthesis and signaling pathways of mosses. PLANT MOLECULAR BIOLOGY 2021; 107:245-277. [PMID: 34245404 DOI: 10.1007/s11103-021-01172-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Most known phytohormones regulate moss development. We present a comprehensive view of the synthesis and signaling pathways for the most investigated of these compounds in mosses, focusing on the model Physcomitrium patens. The last 50 years of research have shown that most of the known phytohormones are synthesized by the model moss Physcomitrium patens (formerly Physcomitrella patens) and regulate its development, in interaction with responses to biotic and abiotic stresses. Biosynthesis and signaling pathways are best described in P. patens for the three classical hormones auxins, cytokinins and abscisic acid. Furthermore, their roles in almost all steps of development, from early filament growth to gametophore development and sexual reproduction, have been the focus of much research effort over the years. Evidence of hormonal roles exist for ethylene and for CLE signaling peptides, as well as for salicylic acid, although their possible effects on development remain unclear. Production of brassinosteroids by P. patens is still debated, and modes of action for these compounds are even less known. Gibberellin biosynthesis and signaling may have been lost in P. patens, while gibberellin precursors such as ent-kaurene derivatives could be used as signals in a yet to discover pathway. As for jasmonic acid, it is not used per se as a hormone in P. patens, but its precursor OPDA appears to play a corresponding role in defense against abiotic stress. We have tried to gather a comprehensive view of the biosynthesis and signaling pathways for all these compounds in mosses, without forgetting strigolactones, the last class of plant hormones to be reported. Study of the strigolactone response in P. patens points to a novel signaling compound, the KAI2-ligand, which was likely employed as a hormone prior to land plant emergence.
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Affiliation(s)
- Ambre Guillory
- INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, 78000, Versailles, France
| | - Sandrine Bonhomme
- INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, 78000, Versailles, France.
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8
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Seven M, Derman ÜC, Harvey AJ. Enzymatic characterization of ancestral/group-IV clade xyloglucan endotransglycosylase/hydrolase enzymes reveals broad substrate specificities. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1660-1673. [PMID: 33825243 DOI: 10.1111/tpj.15262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 05/14/2023]
Abstract
Xyloglucan endotransglycosylase/hydrolase (XTH) enzymes play important roles in cell wall remodelling. Although previous studies have shown a pathway of evolution for XTH genes from bacterial licheninases, through plant endoglucanases (EG16), the order of development within the phylogenetic clades of true XTHs is yet to be elucidated. In addition, recent studies have revealed interesting and potentially useful patterns of transglycosylation beyond the standard xyloglucan-xyloglucan donor/acceptor substrate activities. To study evolutionary relationships and to search for enzymes with useful broad substrate specificities, genes from the 'ancestral' XTH clade of two monocots, Brachypodium distachyon and Triticum aestivum, and two eudicots, Arabidopsis thaliana and Populus tremula, were investigated. Specific activities of the heterologously produced enzymes showed remarkably broad substrate specificities. All the enzymes studied had high activity with the cellulose analogue HEC (hydroxyethyl cellulose) as well as with mixed-link β-glucan as donor substrates, when compared with the standard xyloglucan. Even more surprising was the wide range of acceptor substrates that these enzymes were able to catalyse reactions with, opening a broad range of possible roles for these enzymes, both within plants and in industrial, pharmaceutical and medical fields. Genome screening and expression analyses unexpectedly revealed that genes from this clade were found only in angiosperm genomes and were predominantly or solely expressed in reproductive tissues. We therefore posit that this phylogenetic group is significantly different and should be renamed as the group-IV clade.
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Affiliation(s)
- Merve Seven
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, 34755, Turkey
| | - Ü Cem Derman
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, 34755, Turkey
| | - Andrew J Harvey
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, 34755, Turkey
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Jaeger R, Moody LA. A fundamental developmental transition in Physcomitrium patens is regulated by evolutionarily conserved mechanisms. Evol Dev 2021; 23:123-136. [PMID: 33822471 DOI: 10.1111/ede.12376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 01/15/2023]
Abstract
One of the most defining moments in history was the colonization of land by plants approximately 470 million years ago. The transition from water to land was accompanied by significant changes in the plant body plan, from those than resembled filamentous representatives of the charophytes, the sister group to land plants, to those that were morphologically complex and capable of colonizing harsher habitats. The moss Physcomitrium patens (also known as Physcomitrella patens) is an extant representative of the bryophytes, the earliest land plant lineage. The protonema of P. patens emerges from spores from a chloronemal initial cell, which can divide to self-renew to produce filaments of chloronemal cells. A chloronemal initial cell can differentiate into a caulonemal initial cell, which can divide and self-renew to produce filaments of caulonemal cells, which branch extensively and give rise to three-dimensional shoots. The process by which a chloronemal initial cell differentiates into a caulonemal initial cell is tightly regulated by auxin-induced remodeling of the actin cytoskeleton. Studies have revealed that the genetic mechanisms underpinning this transition also regulate tip growth and differentiation in diverse plant taxa. This review summarizes the known cellular and molecular mechanisms underpinning the chloronema to caulonema transition in P. patens.
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Affiliation(s)
- Richard Jaeger
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Laura A Moody
- Department of Plant Sciences, University of Oxford, Oxford, UK
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Islam M, Inoue T, Hiraide M, Khatun N, Jahan A, Kuwata K, Katagiri S, Umezawa T, Yotsui I, Sakata Y, Takezawa D. Activation of SnRK2 by Raf-like kinase ARK represents a primary mechanism of ABA and abiotic stress responses. PLANT PHYSIOLOGY 2021; 185:533-546. [PMID: 33655297 PMCID: PMC8133623 DOI: 10.1093/plphys/kiaa046] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 11/10/2020] [Indexed: 05/25/2023]
Abstract
The Raf-like protein kinase abscisic acid (ABA) and abiotic stress-responsive Raf-like kinase (ARK) previously identified in the moss Physcomitrium (Physcomitrella) patens acts as an upstream regulator of subgroup III SNF1-related protein kinase2 (SnRK2), the key regulator of ABA and abiotic stress responses. However, the mechanisms underlying activation of ARK by ABA and abiotic stress for the regulation of SnRK2, including the role of ABA receptor-associated group A PP2C (PP2C-A), are not understood. We identified Ser1029 as the phosphorylation site in the activation loop of ARK, which provided a possible mechanism for regulation of its activity. Analysis of transgenic P. patens ark lines expressing ARK-GFP with Ser1029-to-Ala mutation indicated that this replacement causes reductions in ABA-induced gene expression, stress tolerance, and SnRK2 activity. Immunoblot analysis using an anti-phosphopeptide antibody indicated that ABA treatments rapidly stimulate Ser1029 phosphorylation in the wild type (WT). The phosphorylation profile of Ser1029 in ABA-hypersensitive ppabi1 lacking protein phosphatase 2C-A (PP2C-A) was similar to that in the WT, whereas little Ser1029 phosphorylation was observed in ABA-insensitive ark missense mutant lines. Furthermore, newly isolated ppabi1 ark lines showed ABA-insensitive phenotypes similar to those of ark lines. Therefore, ARK is a primary activator of SnRK2, preceding negative regulation by PP2C-A in bryophytes, which provides a prototype mechanism for ABA and abiotic stress responses in plants.
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Affiliation(s)
- Mousona Islam
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
- Plant Tissue Culture Section, Biological Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka 1205, Bangladesh
| | - Takumi Inoue
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Mayuka Hiraide
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Nobiza Khatun
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Akida Jahan
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Sotaro Katagiri
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei City, Tokyo 184-8588, Japan
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei City, Tokyo 184-8588, Japan
| | - Izumi Yotsui
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yoichi Sakata
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Daisuke Takezawa
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
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11
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Komatsu K, Takezawa D, Sakata Y. Decoding ABA and osmostress signalling in plants from an evolutionary point of view. PLANT, CELL & ENVIRONMENT 2020; 43:2894-2911. [PMID: 33459424 DOI: 10.1111/pce.13869] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 05/21/2023]
Abstract
The plant hormone abscisic acid (ABA) is fundamental for land plant adaptation to water-limited conditions. Osmostress, such as drought, induces ABA accumulation in angiosperms, triggering physiological responses such as stomata closure. The core components of angiosperm ABA signalling are soluble ABA receptors, group A protein phosphatase type 2C and SNF1-related protein kinase2 (SnRK2). ABA also has various functions in non-angiosperms, however, suggesting that its role in adaptation to land may not have been angiosperm-specific. Indeed, among land plants, the core ABA signalling components are evolutionarily conserved, implying their presence in a common ancestor. Results of ongoing functional genomics studies of ABA signalling components in bryophytes and algae have expanded our understanding of the evolutionary role of ABA signalling, with genome sequencing uncovering the ABA core module even in algae. In this review, we describe recent discoveries involving the ABA core module in non-angiosperms, tracing the footprints of how ABA evolved as a phytohormone. We also cover the latest findings on Raf-like kinases as upstream regulators of the core ABA module component SnRK2. Finally, we discuss the origin of ABA signalling from an evolutionary perspective.
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Affiliation(s)
- Kenji Komatsu
- Department of Bioresource Development, Tokyo University of Agriculture, Kanagawa, Japan
| | - Daisuke Takezawa
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yoichi Sakata
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
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Jiang S, Zhang H, Ni P, Yu S, Dong H, Zhang A, Cao H, Zhang L, Ruan Y, Cui Z. Genome-Wide Association Study Dissects the Genetic Architecture of Maize Husk Tightness. FRONTIERS IN PLANT SCIENCE 2020; 11:861. [PMID: 32695127 PMCID: PMC7338587 DOI: 10.3389/fpls.2020.00861] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/27/2020] [Indexed: 06/01/2023]
Abstract
The husk is a leafy outer tissue that encloses a maize ear. Previously, we identified the optimum husk structure by measuring the husk length, husk layer number, husk thickness and husk width. Husk tightness (HTI) is a combined trait based on the above four husk measurements. Unveiling the genetic basis of HTI will aid in guiding the genetic improvement of maize for mechanical harvesting and for protecting the ear from pest damage and pathogen infection. Here, we used a maize associate population of 508 inbred lines with tropical, subtropical and temperate backgrounds to analyze the genetic architecture of HTI. Evaluating the phenotypic diversity in three different environments showed that HTI exhibited broad natural variations and a moderate heritability level of 0.41. A diversity analysis indicated that the inbred lines having a temperate background were more loosely related than those having a tropical or subtropical background. HTI showed significant negative correlations with husk thickness and width, which indicates that thicker and wider husks wrapped the ear tighter than thinner and slimmer husks. Combining husk traits with ∼1.25 million single nucleotide polymorphisms in a genome-wide association study revealed 27 variants that were significantly associated with HTI above the threshold of P < 7.26 × 10-6. We found 27 candidate genes for HTI that may participate in (1) husk senescence involving lipid peroxidation (GRMZM2G017616) and programmed cell death (GRMZM2G168898 and GRMZM2G035045); (2) husk morphogenesis involving cell division (GRMZM5G869246) and cell wall architecture (GRMZM2G319798); and (3) cell signal transduction involving protein phosphorylation (GRMZM2G149277 and GRMZM2G004207) and the ABSISIC ACID INSENSITIVE3/VIVIPAROUS1 transcription factor (GRMZM2G088427). These results provide useful information for understanding the genetic basis of husk development. Further studies of identified candidate genes will help elucidate the molecular pathways that regulate HTI in maize.
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Affiliation(s)
- Siqi Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Haibo Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Pengzun Ni
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Haixiao Dong
- College of Plant Sciences, Jilin University, Changchun, China
| | - Ao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Huiying Cao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Lijun Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Zhenhai Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
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Wu J, Ichihashi Y, Suzuki T, Shibata A, Shirasu K, Yamaguchi N, Ito T. Abscisic acid-dependent histone demethylation during postgermination growth arrest in Arabidopsis. PLANT, CELL & ENVIRONMENT 2019; 42:2198-2214. [PMID: 30859592 DOI: 10.1111/pce.13547] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 03/03/2019] [Indexed: 05/22/2023]
Abstract
After germination, seedlings undergo growth arrest in response to unfavourable conditions, a critical adaptation enabling plants to survive harsh environments. The plant hormone abscisic acid (ABA) plays a key role in this arrest. To arrest growth, ABA-dependent transcription factors change gene expression patterns in a flexible and reversible manner. Although the control of gene expression has important roles in growth arrest, the epigenetic mechanisms in the response to ABA are not fully understood. Here, we show that the histone demethylases JUMONJI-C domain-containing protein 30 (JMJ30) and JMJ32 control ABA-mediated growth arrest in Arabidopsis thaliana. During the postgermination stage (2-3 days after germination), the ABA-dependent transcription factor ABA-insensitive3 (ABI3) activates the expression of JMJ30 in response to ABA. JMJ30 then removes a repressive histone mark, H3 lysine 27 trimethylation (H3K27me3), from the SNF1-related protein kinase 2.8 (SnRK2.8) promoter, and hence activates SnRK2.8 expression. SnRK2.8 encodes a kinase that activates ABI3 and is responsible for JMJ30- and JMJ32-mediated growth arrest. A feed-forward loop involving the ABI3 transcription factor, JMJ histone demethylases, and the SnRK2.8 kinase fine-tunes ABA-dependent growth arrest in the postgermination phase. Our findings highlight the importance of the histone demethylases in mediating adaptation of plants to the environment.
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Affiliation(s)
- Jinfeng Wu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Yasunori Ichihashi
- RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi-shi, 332-0012, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501, Japan
| | - Arisa Shibata
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi-shi, 332-0012, Japan
| | - Toshiro Ito
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
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Jahan A, Komatsu K, Wakida-Sekiya M, Hiraide M, Tanaka K, Ohtake R, Umezawa T, Toriyama T, Shinozawa A, Yotsui I, Sakata Y, Takezawa D. Archetypal Roles of an Abscisic Acid Receptor in Drought and Sugar Responses in Liverworts. PLANT PHYSIOLOGY 2019; 179:317-328. [PMID: 30442644 PMCID: PMC6324230 DOI: 10.1104/pp.18.00761] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/27/2018] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA) controls seed dormancy and stomatal closure through binding to the intracellular receptor Pyrabactin resistance1 (Pyr1)/Pyr1-like/regulatory components of ABA receptors (PYR/PYL/RCAR) in angiosperms. Genes encoding PYR/PYL/RCAR are thought to have arisen in the ancestor of embryophytes, but the roles of the genes in nonvascular plants have not been determined. In the liverwort Marchantia polymorpha, ABA reduces growth and enhances desiccation tolerance through increasing accumulation of intracellular sugars and various transcripts such as those of Late Embryogenesis Abundant (LEA)-like genes. In this study, we analyzed a gene designated MpPYL1, which is closely related to PYR/PYL/RCAR of angiosperms, in transgenic liverworts. Transgenic lines overexpressing MpPYL1-GFP showed ABA-hypersensitive growth with enhanced desiccation tolerance, whereas Mppyl1 generated by CRISPR-Cas9-mediated genome editing showed ABA-insensitive growth with reduced desiccation tolerance. Transcriptome analysis indicated that MpPYL1 is a major regulator of abiotic stress-associated genes, including all 35 ABA-induced LEA-like genes. Furthermore, these transgenic plants showed altered responses to extracellular Suc, suggesting that ABA and PYR/PYL/RCAR function in sugar responses. The results presented here reveal an important role of PYR/PYL/RCAR in the ABA response, which was likely acquired in the common ancestor of land plants. The results also indicate the archetypal role of ABA and its receptor in sugar response and accumulation processes for vegetative desiccation tolerance in bryophytes.
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Affiliation(s)
- Akida Jahan
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Kenji Komatsu
- Department of Bioresource Development, Tokyo University of Agriculture, Kanagawa 243-0034, Japan
| | - Mai Wakida-Sekiya
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Mayuka Hiraide
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Keisuke Tanaka
- The NODAI Genome Research Center (NGRC), Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Rumi Ohtake
- The NODAI Genome Research Center (NGRC), Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Tsukasa Toriyama
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Akihisa Shinozawa
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Izumi Yotsui
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yoichi Sakata
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Daisuke Takezawa
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
- Institute for Environmental Science and Technology, Saitama University, Saitama 338-8570, Japan
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An Evolutionarily Conserved Abscisic Acid Signaling Pathway Regulates Dormancy in the Liverwort Marchantia polymorpha. Curr Biol 2018; 28:3691-3699.e3. [PMID: 30416060 DOI: 10.1016/j.cub.2018.10.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/28/2018] [Accepted: 10/04/2018] [Indexed: 01/08/2023]
Abstract
Dormancy is a key process allowing land plants to adapt to changing conditions in the terrestrial habitat, allowing the cessation of growth in response to environmental or physiological cues, entrance into a temporary quiescent state, and subsequent reactivation of growth in more favorable environmental conditions [1-3]. Dormancy may be induced seasonally, sporadically (e.g., in response to drought), or developmentally (e.g., seeds and apical dominance). Asexual propagules, known as gemmae, derived via clonal reproduction in bryophytes, are often dormant until displaced from the parent plant. In the liverwort Marchantia polymorpha, gemmae are produced within specialized receptacles, gemma cups, located on the dorsal side of the vegetative thallus [4]. Mature gemmae are detached from the parent plant but may remain in the cup, with gemma growth suppressed as long as the gemmae remain in the gemma cup and the parental plant is alive [5]. Following dispersal of gemmae from gemma cups by rain, the gemmae germinate in the presence of light and moisture, producing clonal offspring [6]. In land plants, the plant hormone abscisic acid (ABA) regulates many aspects of dormancy and water balance [7]. Here, we demonstrate that ABA plays a central role in the control of gemma dormancy as transgenic M. polymorpha gemmae with reduced sensitivity to ABA fail to establish and/or maintain dormancy. Thus, the common ancestor of land plants used the ABA signaling module to regulate germination of progeny in response to environmental cues, with both gemmae and seeds being derived structures co-opting an ancestral response system.
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Qi Z, Zhang Z, Wang Z, Yu J, Qin H, Mao X, Jiang H, Xin D, Yin Z, Zhu R, Liu C, Yu W, Hu Z, Wu X, Liu J, Chen Q. Meta-analysis and transcriptome profiling reveal hub genes for soybean seed storage composition during seed development. PLANT, CELL & ENVIRONMENT 2018; 41:2109-2127. [PMID: 29486529 DOI: 10.1111/pce.13175] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/10/2018] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Soybean is an important crop providing edible oil and protein source. Soybean oil and protein contents are quantitatively inherited and significantly affected by environmental factors. In this study, meta-analysis was conducted based on soybean physical maps to integrate quantitative trait loci (QTLs) from multiple experiments in different environments. Meta-QTLs for seed oil, fatty acid composition, and protein were identified. Of them, 11 meta-QTLs were located on hot regions for both seed oil and protein. Next, we selected 4 chromosome segment substitution lines with different seed oil and protein contents to characterize their 3 years of phenotype selection in the field. Using strand-specific RNA-sequencing analysis, we profile the time-course transcriptome patterns of soybean seeds at early maturity, middle maturity, and dry seed stages. Pairwise comparison and K-means clustering analysis revealed 7,482 differentially expressed genes and 45 expression patterns clusters. Weighted gene coexpression network analysis uncovered 46 modules of gene expression patterns. The 2 most significant coexpression networks were visualized, and 7 hub genes were identified that were involved in soybean oil and seed storage protein accumulation processes. Our results provided a transcriptome dataset for soybean seed development, and the candidate hub genes represent a foundation for further research.
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Affiliation(s)
- Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhanguo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhongyu Wang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jingyao Yu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Hongtao Qin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Xinrui Mao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Hongwei Jiang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhengong Yin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Rongsheng Zhu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Wei Yu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Zhenbang Hu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
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17
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Mechanisms Underlying Freezing and Desiccation Tolerance in Bryophytes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:167-187. [DOI: 10.1007/978-981-13-1244-1_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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18
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Xiao L, Yobi A, Koster KL, He Y, Oliver MJ. Desiccation tolerance in Physcomitrella patens: Rate of dehydration and the involvement of endogenous abscisic acid (ABA). PLANT, CELL & ENVIRONMENT 2018; 41:275-284. [PMID: 29105792 DOI: 10.1111/pce.13096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 05/13/2023]
Abstract
The moss Physcomitrella patens, a model system for basal land plants, tolerates several abiotic stresses, including dehydration. We previously reported that Physcomitrella patens survives equilibrium dehydration to -13 MPa in a closed system at 91% RH. Tolerance of desiccation to water potentials below -100 MPa was only achieved by pretreatment with exogenous abscisic acid (ABA). We report here that gametophores, but not protonemata, can survive desiccation below -100 MPa after a gradual drying regime in an open system, without exogenous ABA. In contrast, faster equilibrium drying at 90% RH for 3-5 days did not induce desiccation tolerance in either tissue. Endogenous ABA accumulated in protonemata and gametophores under both drying regimes, so did not correlate directly with desiccation tolerance. Gametophores of a Ppabi3a/b/c triple knock out transgenic line also survived the gradual dehydration regime, despite impaired ABA signaling. Our results suggest that the initial drying rate, and not the amount of endogenous ABA, may be critical in the acquisition of desiccation tolerance. Results from this work will provide insight into ongoing studies to uncover the role of ABA in the dehydration response and the underlying mechanisms of desiccation tolerance in this bryophyte.
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Affiliation(s)
- Lihong Xiao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, 311300, China
- School of Life Sciences, Capital Normal University, Beijing, 100048, China
- U.S. Department of Agriculture - Agricultural Research Service, Plant Genetic Research Unit, University of Missouri, Columbia, MO, 65211, USA
| | - Abou Yobi
- U.S. Department of Agriculture - Agricultural Research Service, Plant Genetic Research Unit, University of Missouri, Columbia, MO, 65211, USA
| | - Karen L Koster
- Department of Biology, University of South Dakota, Vermillion, SD, 57069, USA
| | - Yikun He
- School of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Melvin J Oliver
- U.S. Department of Agriculture - Agricultural Research Service, Plant Genetic Research Unit, University of Missouri, Columbia, MO, 65211, USA
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Carbonero P, Iglesias-Fernández R, Vicente-Carbajosa J. The AFL subfamily of B3 transcription factors: evolution and function in angiosperm seeds. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:871-880. [PMID: 28007955 DOI: 10.1093/jxb/erw458] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Seed development follows zygotic embryogenesis; during the maturation phase reserves accumulate and desiccation tolerance is acquired. This is tightly regulated at the transcriptional level and the AFL (ABI3/FUS3/LEC2) subfamily of B3 transcription factors (TFs) play a central role. They alter hormone biosynthesis, mainly in regards to abscisic acid and gibberellins, and also regulate the expression of other TFs and/or modulate their downstream activity via protein-protein interactions. This review deals with the origin of AFL TFs, which can be traced back to non-vascular plants such as Physcomitrella patens and achieves foremost expansion in the angiosperms. In green algae, like the unicellular Chlamydomonas reinhardtii or the pluricellular Klebsormidium flaccidum, a single B3 gene and four B3 paralogous genes are annotated, respectively. However, none of them present with the structural features of the AFL subfamily, with the exception of the B3 DNA-binding domain. Phylogenetic analysis groups the AFL TFs into four Major Clusters of Ortologous Genes (MCOGs). The origin and function of these genes is discussed in view of their expression patterns and in the context of major regulatory interactions in seeds of monocotyledonous and dicotyledonous species.
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Affiliation(s)
- Pilar Carbonero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
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20
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Tan T, Sun Y, Peng X, Wu G, Bao F, He Y, Zhou H, Lin H. ABSCISIC ACID INSENSITIVE3 Is Involved in Cold Response and Freezing Tolerance Regulation in Physcomitrella patens. FRONTIERS IN PLANT SCIENCE 2017; 8:1599. [PMID: 28955377 PMCID: PMC5601040 DOI: 10.3389/fpls.2017.01599] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/31/2017] [Indexed: 05/08/2023]
Abstract
Synopsis This work demonstrates that PpABI3 contributes to freezing tolerance regulation in Physcomitrella patens. Transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3) is known to play a major role in regulating seed dormancy, germination, seedling development as well as stress responses. ABI3 is conserved among land plants; however, its roles in non-seed plants under stress conditions have not been well characterized. In this study, we report that ABI3 is involved in freezing tolerance regulation during cold acclimation at least in part through ABA signaling pathway in moss Physcomitrella patens (P. patens). Deletion of PpABI3 (Δabi3-1) compromises the induction of genes related to cold response and antioxidative protection, resulting in reduced accumulation of cryoprotectants and antioxidants. In addition, photosystem II (PSII) activity is repressed in Δabi3-1 during cold acclimation partially due to alternations of photosynthetic protein complexes compositions. The gametophyte of Δabi3-1 displays severe growth inhibition and developmental deficiency under low temperature condition, while two independent complementary lines display phenotypes similar to that of wild-type P. patens (WT). Furthermore, the freezing tolerance of Δabi3-1 was significantly affected by deletion of PpABI3. These data revealed that PpABI3 plays an important role in low temperature response and freezing tolerance in P. patens.
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Affiliation(s)
- Tinghong Tan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
| | - Yanni Sun
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
| | - Xingji Peng
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
| | - Guochun Wu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
| | - Fang Bao
- School of Life Sciences, Capital Normal UniversityBeijing, China
| | - Yikun He
- School of Life Sciences, Capital Normal UniversityBeijing, China
| | - Huapeng Zhou
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
- *Correspondence: Huapeng Zhou
| | - Honghui Lin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
- Honghui Lin
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21
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Stevenson SR, Kamisugi Y, Trinh CH, Schmutz J, Jenkins JW, Grimwood J, Muchero W, Tuskan GA, Rensing SA, Lang D, Reski R, Melkonian M, Rothfels CJ, Li FW, Larsson A, Wong GKS, Edwards TA, Cuming AC. Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance. THE PLANT CELL 2016; 28:1310-27. [PMID: 27194706 PMCID: PMC4944411 DOI: 10.1105/tpc.16.00091] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/18/2016] [Accepted: 05/13/2016] [Indexed: 05/19/2023]
Abstract
The anatomically simple plants that first colonized land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA nonresponsive mutants in the model bryophyte Physcomitrella patens and genotyped a segregating population to map and identify the ABA NON-RESPONSIVE (ANR) gene encoding a modular protein kinase comprising an N-terminal PAS domain, a central EDR domain, and a C-terminal MAPKKK-like domain. anr mutants fail to accumulate dehydration tolerance-associated gene products in response to drought, ABA, or osmotic stress and do not acquire ABA-dependent desiccation tolerance. The crystal structure of the PAS domain, determined to 1.7-Å resolution, shows a conserved PAS-fold that dimerizes through a weak dimerization interface. Targeted mutagenesis of a conserved tryptophan residue within the PAS domain generates plants with ABA nonresponsive growth and strongly attenuated ABA-responsive gene expression, whereas deleting this domain retains a fully ABA-responsive phenotype. ANR orthologs are found in early-diverging land plant lineages and aquatic algae but are absent from more recently diverged vascular plants. We propose that ANR genes represent an ancestral adaptation that enabled drought stress survival of the first terrestrial colonizers but were lost during land plant evolution.
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Affiliation(s)
- Sean R Stevenson
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Jerry W Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Jane Grimwood
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Stefan A Rensing
- University of Marburg, Plant Cell Biology, D-35043 Marburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Daniel Lang
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Ralf Reski
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | | | - Carl J Rothfels
- Department of Integrative Biology, University of California, Berkeley California 94720-3140
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Anders Larsson
- Uppsala University, Systematic Biology, 752 36 Uppsala, Sweden
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada BGI-Shenzhen, Shenzhen 518083, China
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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22
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Ghosh TK, Kaneko M, Akter K, Murai S, Komatsu K, Ishizaki K, Yamato KT, Kohchi T, Takezawa D. Abscisic acid-induced gene expression in the liverwort Marchantia polymorpha is mediated by evolutionarily conserved promoter elements. PHYSIOLOGIA PLANTARUM 2016; 156:407-20. [PMID: 26456006 DOI: 10.1111/ppl.12385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 07/04/2015] [Accepted: 07/17/2015] [Indexed: 05/23/2023]
Abstract
Abscisic acid (ABA) is a phytohormone widely distributed among members of the land plant lineage (Embryophyta), regulating dormancy, stomata closure and tolerance to environmental stresses. In angiosperms (Magnoliophyta), ABA-induced gene expression is mediated by promoter elements such as the G-box-like ACGT-core motifs recognized by bZIP transcription factors. In contrast, the mode of regulation by ABA of gene expression in liverworts (Marchantiophyta), representing one of the earliest diverging land plant groups, has not been elucidated. In this study, we used promoters of the liverwort Marchantia polymorpha dehydrin and the wheat Em genes fused to the β-glucuronidase (GUS) reporter gene to investigate ABA-induced gene expression in liverworts. Transient assays of cultured cells of Marchantia indicated that ACGT-core motifs proximal to the transcription initiation site play a role in the ABA-induced gene expression. The RY sequence recognized by B3 transcriptional regulators was also shown to be responsible for the ABA-induced gene expression. In transgenic Marchantia plants, ABA treatment elicited an increase in GUS expression in young gemmalings, which was abolished by simultaneous disruption of the ACGT-core and RY elements. ABA-induced GUS expression was less obvious in mature thalli than in young gemmalings, associated with reductions in sensitivity to exogenous ABA during gametophyte growth. In contrast, lunularic acid, which had been suggested to function as an ABA-like substance, had no effect on GUS expression. The results demonstrate the presence of ABA-specific response mechanisms mediated by conserved cis-regulatory elements in liverworts, implying that the mechanisms had been acquired in the common ancestors of embryophytes.
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Affiliation(s)
- Totan K Ghosh
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Midori Kaneko
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Khaleda Akter
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Shuhei Murai
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kenji Komatsu
- Department of Bioproduction Technology, Junior College of Tokyo University of Agriculture, Tokyo, Japan
| | | | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Engineering, Kinki University, Higashiosaka, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Daisuke Takezawa
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
- Institute for Environmental Science and Technology, Saitama University, Saitama, Japan
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23
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Yasumura Y, Pierik R, Kelly S, Sakuta M, Voesenek LACJ, Harberd NP. An Ancestral Role for CONSTITUTIVE TRIPLE RESPONSE1 Proteins in Both Ethylene and Abscisic Acid Signaling. PLANT PHYSIOLOGY 2015; 169:283-98. [PMID: 26243614 PMCID: PMC4577374 DOI: 10.1104/pp.15.00233] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/23/2015] [Indexed: 05/20/2023]
Abstract
Land plants have evolved adaptive regulatory mechanisms enabling the survival of environmental stresses associated with terrestrial life. Here, we focus on the evolution of the regulatory CONSTITUTIVE TRIPLE RESPONSE1 (CTR1) component of the ethylene signaling pathway that modulates stress-related changes in plant growth and development. First, we compare CTR1-like proteins from a bryophyte, Physcomitrella patens (representative of early divergent land plants), with those of more recently diverged lycophyte and angiosperm species (including Arabidopsis [Arabidopsis thaliana]) and identify a monophyletic CTR1 family. The fully sequenced P. patens genome encodes only a single member of this family (PpCTR1L). Next, we compare the functions of PpCTR1L with that of related angiosperm proteins. We show that, like angiosperm CTR1 proteins (e.g. AtCTR1 of Arabidopsis), PpCTR1L modulates downstream ethylene signaling via direct interaction with ethylene receptors. These functions, therefore, likely predate the divergence of the bryophytes from the land-plant lineage. However, we also show that PpCTR1L unexpectedly has dual functions and additionally modulates abscisic acid (ABA) signaling. In contrast, while AtCTR1 lacks detectable ABA signaling functions, Arabidopsis has during evolution acquired another homolog that is functionally distinct from AtCTR1. In conclusion, the roles of CTR1-related proteins appear to have functionally diversified during land-plant evolution, and angiosperm CTR1-related proteins appear to have lost an ancestral ABA signaling function. Our study provides new insights into how molecular events such as gene duplication and functional differentiation may have contributed to the adaptive evolution of regulatory mechanisms in plants.
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Affiliation(s)
- Yuki Yasumura
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (Y.Y., S.K., N.P.H.); Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.S.); and Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (R.P., L.A.C.J.V.)
| | - Ronald Pierik
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (Y.Y., S.K., N.P.H.); Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.S.); and Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (R.P., L.A.C.J.V.)
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (Y.Y., S.K., N.P.H.); Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.S.); and Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (R.P., L.A.C.J.V.)
| | - Masaaki Sakuta
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (Y.Y., S.K., N.P.H.); Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.S.); and Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (R.P., L.A.C.J.V.)
| | - Laurentius A C J Voesenek
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (Y.Y., S.K., N.P.H.); Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.S.); and Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (R.P., L.A.C.J.V.)
| | - Nicholas P Harberd
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (Y.Y., S.K., N.P.H.); Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.S.); and Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (R.P., L.A.C.J.V.)
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24
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Cuming AC, Stevenson SR. From pond slime to rain forest: the evolution of ABA signalling and the acquisition of dehydration tolerance. THE NEW PHYTOLOGIST 2015; 206:5-7. [PMID: 25711244 DOI: 10.1111/nph.13333] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Andrew C Cuming
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sean R Stevenson
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
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25
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Tavakol E, Sardaro MLS, Shariati JV, Rossini L, Porceddu E. Isolation, promoter analysis and expression profile of Dreb2 in response to drought stress in wheat ancestors. Gene 2014; 549:24-32. [PMID: 25017054 DOI: 10.1016/j.gene.2014.07.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/25/2014] [Accepted: 07/09/2014] [Indexed: 11/18/2022]
Abstract
Drought is one of the most important abiotic stresses, constraining crop production seriously. The dehydration responsive element binding proteins (DREBs) are important plant-specific transcription factors that respond to various abiotic stresses and consequently induce abiotic stress-related genes that impart stress endurance in plants. Wild species are naturally exposed to various abiotic stresses and potentially harbor suitable alleles through natural selection. In this study we isolated and characterized Dreb2 from Triticum urartu (GenBank: KF731664), Aegilops speltoides (GenBank: KF731665) and Aegilops tauschii (GenBank: KF731663), the A, B and D genome ancestors of bread wheat, respectively. Analysis of over 1.3 kb upstream region of the gene revealed the presence of several conserved cis-acting regulatory elements including ABA-responsive elements, low temperature responsive elements, and several light and environmental signaling related motifs potentially vindicate Dreb2 responses to environmental signals. Moreover, the gene exhibited an alternative splicing, conserved among orthologous genes in grasses, and produced a non-functional isoform due to splicing in an exon resulted frame-shift creating an early stop codon before the functional domain. The expression analysis of Dreb2 under normal and different levels of dehydration stress conditions indicated that the two active spliced isoforms are upregulated when the plant exposed to drought stress whereas the non-functional isoform is downregulated in severe drought.
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Affiliation(s)
- Elahe Tavakol
- Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy.
| | - Maria Luisa Savo Sardaro
- University of Parma, Department of Food Science, Parco Area delle Scienze 49A, 43124 Parma, Italy
| | - J Vahid Shariati
- National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran
| | - Laura Rossini
- Università degli Studi di Milano, DISAA, Via Celoria 2, 20133 Milan
| | - Enrico Porceddu
- Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy; University of Tuscia, Department of Agrobiology and Agrochemistry, Viterbo
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26
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27
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Lim S, Park J, Lee N, Jeong J, Toh S, Watanabe A, Kim J, Kang H, Kim DH, Kawakami N, Choi G. ABA-insensitive3, ABA-insensitive5, and DELLAs Interact to activate the expression of SOMNUS and other high-temperature-inducible genes in imbibed seeds in Arabidopsis. THE PLANT CELL 2013. [PMID: 24326588 DOI: 10.1105/tpc.113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Seeds monitor the environment to germinate at the proper time, but different species respond differently to environmental conditions, particularly light and temperature. In Arabidopsis thaliana, light promotes germination but high temperature suppresses germination. We previously reported that light promotes germination by repressing SOMNUS (SOM). Here, we examined whether high temperature also regulates germination through SOM and found that high temperature activates SOM expression. Consistent with this, som mutants germinated more frequently than the wild type at high temperature. The induction of SOM mRNA at high temperature required abscisic acid (ABA) and gibberellic acid biosynthesis, and ABA-insensitive3 (ABI3), ABI5, and DELLAs positively regulated SOM expression. Chromatin immunoprecipitation assays indicated that ABI3, ABI5, and DELLAs all target the SOM promoter. At the protein level, ABI3, ABI5, and DELLAs all interact with each other, suggesting that they form a complex on the SOM promoter to activate SOM expression at high temperature. We found that high-temperature-inducible genes frequently have RY motifs and ABA-responsive elements in their promoters, some of which are targeted by ABI3, ABI5, and DELLAs in vivo. Taken together, our data indicate that ABI3, ABI5, and DELLAs mediate high-temperature signaling to activate the expression of SOM and other high-temperature-inducible genes, thereby inhibiting seed germination.
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Affiliation(s)
- Soohwan Lim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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28
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Lim S, Park J, Lee N, Jeong J, Toh S, Watanabe A, Kim J, Kang H, Kim DH, Kawakami N, Choi G. ABA-insensitive3, ABA-insensitive5, and DELLAs Interact to activate the expression of SOMNUS and other high-temperature-inducible genes in imbibed seeds in Arabidopsis. THE PLANT CELL 2013; 25:4863-78. [PMID: 24326588 PMCID: PMC3903992 DOI: 10.1105/tpc.113.118604] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/07/2013] [Accepted: 11/16/2013] [Indexed: 05/18/2023]
Abstract
Seeds monitor the environment to germinate at the proper time, but different species respond differently to environmental conditions, particularly light and temperature. In Arabidopsis thaliana, light promotes germination but high temperature suppresses germination. We previously reported that light promotes germination by repressing SOMNUS (SOM). Here, we examined whether high temperature also regulates germination through SOM and found that high temperature activates SOM expression. Consistent with this, som mutants germinated more frequently than the wild type at high temperature. The induction of SOM mRNA at high temperature required abscisic acid (ABA) and gibberellic acid biosynthesis, and ABA-insensitive3 (ABI3), ABI5, and DELLAs positively regulated SOM expression. Chromatin immunoprecipitation assays indicated that ABI3, ABI5, and DELLAs all target the SOM promoter. At the protein level, ABI3, ABI5, and DELLAs all interact with each other, suggesting that they form a complex on the SOM promoter to activate SOM expression at high temperature. We found that high-temperature-inducible genes frequently have RY motifs and ABA-responsive elements in their promoters, some of which are targeted by ABI3, ABI5, and DELLAs in vivo. Taken together, our data indicate that ABI3, ABI5, and DELLAs mediate high-temperature signaling to activate the expression of SOM and other high-temperature-inducible genes, thereby inhibiting seed germination.
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Affiliation(s)
- Soohwan Lim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Jeongmoo Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Nayoung Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Jinkil Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Shigeo Toh
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Asuka Watanabe
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Junghyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Hyojin Kang
- National Institute of Supercomputing and Networking, Korea Institute of Science and Technology Information, Daejeon 305-806, Korea
| | - Dong Hwan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Naoto Kawakami
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
- Address correspondence to
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Yotsui I, Saruhashi M, Kawato T, Taji T, Hayashi T, Quatrano RS, Sakata Y. ABSCISIC ACID INSENSITIVE3 regulates abscisic acid-responsive gene expression with the nuclear factor Y complex through the ACTT-core element in Physcomitrella patens. THE NEW PHYTOLOGIST 2013; 199:101-109. [PMID: 23550615 DOI: 10.1111/nph.12251] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 02/25/2013] [Indexed: 05/10/2023]
Abstract
The phytohormone ABA and the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3)/VIVIPAROUS 1 (VP1) function in protecting embryos during the desiccation stage of seed development. In a similar signaling pathway, vegetative tissue of the moss Physcomitrella patens survives desiccation by activating downstream genes (e.g. LEA1) in response to ABA and ABI3. We show that the PpLEA1 promoter responds to PpABI3 primarily through the ACTT-core element (5'-TCCACTTGTC-3'), while the ACGT-core ABA-responsive element (ABRE) appears to respond to ABA alone. We also found by yeast-two-hybrid screening that PpABI3A interacts with PpNF-YC1, a subunit of CCAAT box binding factor (CBF)/nuclear factor Y (NF-Y). PpNF-YC1 increased the activation of the PpLEA1 promoter when incubated with PpABI3A, as did NF-YB, NF-YC, and ABI3 from Arabidopsis. This new response element (ACTT) is responsible for activating the ABI3-dependent ABA response pathway cooperatively with the nuclear factor Y (NF-Y) complex. These results further define the regulatory interactions at the transcriptional level for the expression of this network of genes required for drought/desiccation tolerance. This gene regulatory set is in large part conserved between vegetative tissue of bryophytes and seeds of angiosperms and will shed light on the evolution of this pathway in the green plant lineage.
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Affiliation(s)
- Izumi Yotsui
- Department of BioScience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagayaku, Tokyo, 156-8502, Japan
| | - Masashi Saruhashi
- Department of BioScience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagayaku, Tokyo, 156-8502, Japan
| | - Takahiro Kawato
- Department of BioScience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagayaku, Tokyo, 156-8502, Japan
| | - Teruaki Taji
- Department of BioScience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagayaku, Tokyo, 156-8502, Japan
| | - Takahisa Hayashi
- Department of BioScience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagayaku, Tokyo, 156-8502, Japan
| | - Ralph S Quatrano
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130-4899, USA
| | - Yoichi Sakata
- Department of BioScience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagayaku, Tokyo, 156-8502, Japan
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30
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Bonhomme S, Nogué F, Rameau C, Schaefer DG. Usefulness of Physcomitrella patens for studying plant organogenesis. Methods Mol Biol 2013; 959:21-43. [PMID: 23299666 DOI: 10.1007/978-1-62703-221-6_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this chapter, we review the main organogenesis features and associated regulation processes of the moss Physcomitrella patens (P. patens), the model plant for the Bryophytes. We highlight how the study of this descendant of the earliest plant species that colonized earth, brings useful keys to understand the mechanisms that determine and control both vascular and non vascular plants organogenesis. Despite its simple morphogenesis pattern, P. patens still requires the fine tuning of organogenesis regulators, including hormone signalling, common to the whole plant kingdom, and which study is facilitated by a high number of molecular tools, among which the powerful possibility of gene targeting/replacement. The recent discovery of moss cells reprogramming capacity completes the picture of an excellent model for studying plant organogenesis.
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Affiliation(s)
- Sandrine Bonhomme
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France.
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31
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Domozych DS. The quest for four-dimensional imaging in plant cell biology: it's just a matter of time. ANNALS OF BOTANY 2012; 110:461-74. [PMID: 22628381 PMCID: PMC3394652 DOI: 10.1093/aob/mcs107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 04/04/2012] [Indexed: 05/22/2023]
Abstract
BACKGROUND Analysis of plant cell dynamics over time, or four-dimensional imaging (4-DI), represents a major goal of plant science. The ability to resolve structures in the third dimension within the cell or tissue during developmental events or in response to environmental or experimental stresses (i.e. 4-DI) is critical to our understanding of gene expression, post-expression modulations of macromolecules and sub-cellular system interactions. SCOPE Microscopy-based technologies have been profoundly integral to this type of investigation, and new and refined microscopy technologies now allow for the visualization of cell dynamics with unprecedented resolution, contrast and experimental versatility. However, certain realities of light and electron microscopy, choice of specimen and specimen preparation techniques limit the scope of readily attaining 4-DI. Today, the plant microscopist must use a combinatorial strategy whereby multiple microscopy-based investigations are used. Modern fluorescence, confocal laser scanning, transmission electron and scanning electron microscopy provide effective conduits for synthesizing data detailing live cell dynamics and highly resolved snapshots of specific cell structures that will ultimately lead to 4-DI. This review provides a synopsis of such technologies available.
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Affiliation(s)
- David S Domozych
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, NY 12866, USA.
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32
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Takezawa D, Komatsu K, Sakata Y. ABA in bryophytes: how a universal growth regulator in life became a plant hormone? JOURNAL OF PLANT RESEARCH 2011; 124:437-53. [PMID: 21416316 DOI: 10.1007/s10265-011-0410-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 02/11/2011] [Indexed: 05/03/2023]
Abstract
Abscisic acid (ABA) is not a plant-specific compound but one found in organisms across kingdoms from bacteria to animals, suggesting that it is a ubiquitous and versatile substance that can modulate physiological functions of various organisms. Recent studies have shown that plants developed an elegant system for ABA sensing and early signal transduction mechanisms to modulate responses to environmental stresses for survival in terrestrial conditions. ABA-induced increase in stress tolerance has been reported not only in vascular plants but also in non-vascular bryophytes. Since bryophytes are the key group of organisms in the context of plant evolution, clarification of their ABA-dependent processes is important for understanding evolutionary adaptation of land plants. Molecular approaches using Physcomitrella patens have revealed that ABA plays a role in dehydration stress tolerance in mosses, which comprise a major group of bryophytes. Furthermore, we recently reported that signaling machinery for ABA responses is also conserved in liverworts, representing the most basal members of extant land plant lineage. Conservation of the mechanism for ABA sensing and responses in angiosperms and basal land plants suggests that acquisition of this mechanism for stress tolerance in vegetative tissues was one of the critical evolutionary events for adaptation to the land. This review describes the role of ABA in basal land plants as well as non-land plant organisms and further elaborates on recent progress in molecular studies of model bryophytes by comparative and functional genomic approaches.
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Affiliation(s)
- Daisuke Takezawa
- Graduate School of Science and Engineering, Institute for Environmental Science and Technology, Saitama University, Saitama 338-8570, Japan.
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Timmerhaus G, Hanke ST, Buchta K, Rensing SA. Prediction and validation of promoters involved in the abscisic acid response in Physcomitrella patens. MOLECULAR PLANT 2011; 4:713-29. [PMID: 21398384 DOI: 10.1093/mp/ssr009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Detection of cis-regulatory elements, such as transcription factor binding sites (TFBS), through utilization of ortholog conservation is possible only if genomic data from closely related organisms are available. An alternative approach is the detection of TFBS based on their overrepresentation in promoters of co-regulated genes. However, this approach usually suffers from a high rate of false-positive prediction. Here, we have conducted a case study using promoters of genes known to be strongly induced by the phytohormone abscisic acid (ABA) in the model plant Physcomitrella patens, a moss. Putative TFBS were detected using three de novo motif detection tools in a strict consensus approach. The resulting motifs were validated using data from microarray expression profiling and were able to predict ABA-induced genes with high specificity (90.48%) at mediocre sensitivity (33.33%). In addition, 27 genes predicted to contain ABA-responsive TFBS were validated using real-time PCR. Here, a total of 37% of the genes could be shown to be induced upon ABA treatment, while 70% were found to be regulated by ABA. We conclude that the consensus approach for motif detection using co-regulation information can be used to identify genes that are regulated under a given stimulus. In terms of evolution, we find that the ABA response has apparently been conserved since the first land plants on the level of families involved in transcriptional regulation.
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Affiliation(s)
- Gerrit Timmerhaus
- Faculty of Biology, University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany
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Xu ZS, Chen M, Li LC, Ma YZ. Functions and application of the AP2/ERF transcription factor family in crop improvement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:570-85. [PMID: 21676172 DOI: 10.1111/j.1744-7909.2011.01062.x] [Citation(s) in RCA: 219] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants have acquired sophisticated stress response systems to adapt to changing environments. It is important to understand plants' stress response mechanisms in the effort to improve crop productivity under stressful conditions. The AP2/ERF transcription factors are known to regulate diverse processes of plant development and stress responses. In this study, the molecular characteristics and biological functions of AP2/ERFs in a variety of plant species were analyzed. AP2/ERFs, especially those in DREB and ERF subfamilies, are ideal candidates for crop improvement because their overexpression enhances tolerances to drought, salt, freezing, as well as resistances to multiple diseases in the transgenic plants. The comprehensive analysis of physiological functions is useful in elucidating the biological roles of AP2/ERF family genes in gene interaction, pathway regulation, and defense response under stress environments, which should provide new opportunities for the crop tolerance engineering.
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Affiliation(s)
- Zhao-Shi Xu
- National Key Facility of Crop Gene Resources and Genetic Improvement (NFCRI), Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China
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