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Cheng YJ, Wang JW, Ye R. Histone dynamics responding to internal and external cues underlying plant development. PLANT PHYSIOLOGY 2024; 194:1980-1997. [PMID: 38124490 DOI: 10.1093/plphys/kiad676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Plants necessitate a refined coordination of growth and development to effectively respond to external triggers for survival and successful reproduction. This intricate harmonization of plant developmental processes and adaptability hinges on significant alterations within their epigenetic landscapes. In this review, we first delve into recent strides made in comprehending underpinning the dynamics of histones, driven by both internal and external cues. We encapsulate the prevailing working models through which cis/trans elements navigate the acquisition and removal of histone modifications, as well as the substitution of histone variants. As we look ahead, we anticipate that delving deeper into the dynamics of epigenetic regulation at the level of individual cells or specific cell types will significantly enrich our comprehension of how plant development unfolds under the influence of internal and external cues. Such exploration holds the potential to provide unprecedented resolution in understanding the orchestration of plant growth and development.
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Affiliation(s)
- Ying-Juan Cheng
- College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- New Cornerstone Science Laboratory, Shanghai 200032, China
| | - Ruiqiang Ye
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
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Titova MV, Lunkova MK, Tyurina TM, Prudnikova ON, Popova EV, Klychnikov OI, Metalnikov PS, Ikhalaynen YA, Vasileva EN, Rodin IA, Nosov AM. Suspension cell cultures of Panax vietnamensis as a biotechnological source of ginsenosides: growth, cytology, and ginsenoside profile assessment. FRONTIERS IN PLANT SCIENCE 2024; 15:1349494. [PMID: 38469323 PMCID: PMC10926444 DOI: 10.3389/fpls.2024.1349494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/25/2024] [Indexed: 03/13/2024]
Abstract
Introduction Panax vietnamensis is a valuable medicinal plant and a source of a broad spectrum of biologically active ginsenosides of different structural groups. Overexploitation and low adaptability to planation cultivation have made this species vulnerable to human pressure and prompted the development of cell cultivation in vitro as a sustainable alternative to harvesting wild plants for their bioactive components. Despite high interest in biotechnological production, little is known about the main factors affecting cell growth and ginsenoside biosynthesis of this species under in vitro conditions. In this study, the potential of cell cultures of P. vietnamensis as a biotechnological source of ginsenosides was was assessed. Methods Six suspension cell lines that were developed from different sections of a single rhizome through a multi-step culture optimization process and maintained for over 3 years on media with different mineral salt base and varying contents of auxins and cytokinins. These cell lines were evaluated for productivity parameters and cytological characteristics. Ginsenoside profiles were assessed using a combination of the reversed-phase ultra-high-performance liquid chromatography-Orbitrap-tandem mass spectrometry (UHPLC-Orbitrap-MS/MS) and ultra-performance liquid chromatography-time of flight-mass spectrometry (UPLC-TOF-MS). Results All lines demonstrated good growth with a specific growth rate of 0.1-0.2 day-1, economic coefficient of 0.31-0.70, productivity on dry weight (DW) of 0.30-0.83 gDW (L·day)-1, and maximum biomass accumulation varying from 10 to 22 gDW L-1. Ginsenosides of the protopanaxadiol (Rb1, Rb2/Rb3, malonyl-Rb1, and malonyl-Rb2/Rb3), oleanolic acid (R0 and chikusetsusaponin IV), and ocotillol (vinaginsenoside R1) groups and their isomers were identified in cell biomass extracts. Chikusetsusaponin IV was identified in P. vietnamensis cell culture for the first time. Discussion These results suggest that suspension cell cultures of Vietnamese ginseng have a high potential for the biotechnological production of biomass containing ginsenosides, particularly of the oleanolic acid and ocotillol groups.
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Affiliation(s)
- Maria V. Titova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Maria K. Lunkova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana M. Tyurina
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Olga N. Prudnikova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Elena V. Popova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Oleg I. Klychnikov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
- Department of Biochemistry, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Pavel S. Metalnikov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri A. Ikhalaynen
- Department of Analytical Chemistry, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Elizaveta N. Vasileva
- Department of Analytical Chemistry, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Igor A. Rodin
- Department of Analytical Chemistry, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander M. Nosov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
- Department of Plant Physiology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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Guo Z, Bai Y, Zhang X, Guo L, Zhu L, Sun D, Sun K, Xu X, Yang X, Xie W, Wang S, Wu Q, Crickmore N, Zhou X, Zhang Y. RNA m 6 A Methylation Suppresses Insect Juvenile Hormone Degradation to Minimize Fitness Costs in Response to A Pathogenic Attack. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307650. [PMID: 38087901 PMCID: PMC10853702 DOI: 10.1002/advs.202307650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/05/2023] [Indexed: 02/10/2024]
Abstract
Bioinsecticides and transgenic crops based on the bacterial pathogen Bacillus thuringiensis (Bt) can effectively control diverse agricultural insect pests, nevertheless, the evolution of resistance without obvious fitness costs has seriously eroded the sustainable use of these Bt products. Recently, it has been discovered that an increased titer of juvenile hormone (JH) favors an insect host (Plutella xylostella) to enhance fitness whilst resisting the Bt pathogen, however, the underlying regulatory mechanisms of the increased JH titer are obscure. Here, the involvement of N6 -methyladenosine (m6 A) RNA modification in modulating the availability of JH in this process is defined. Specifically, it is found that two m6 A methyltransferase subunit genes, PxMettl3 and PxMettl14, repress the expression of a key JH-degrading enzyme JH esterase (JHE) to induce an increased JH titer, mitigating the fitness costs associated with a robust defense against the Bt pathogen. This study identifies an as-yet uncharacterized m6 A-mediated epigenetic regulator of insect hormones for maintaining fitness during pathogen defense and unveils an emerging Bt resistance-related m6 A methylation atlas in insects, which further expands the functional landscape of m6 A modification and showcases the pivotal role of epigenetic regulation in host-pathogen interactions.
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Affiliation(s)
- Zhaojiang Guo
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Yang Bai
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Xinyi Zhang
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Le Guo
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Liuhong Zhu
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Dan Sun
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Kaiyue Sun
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Xudan Xu
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Xin Yang
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Wen Xie
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Shaoli Wang
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Qingjun Wu
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
| | - Neil Crickmore
- School of Life SciencesUniversity of SussexBrightonBN1 9QGUK
| | - Xuguo Zhou
- Department of EntomologyUniversity of KentuckyLexingtonKentucky40546‐0091USA
| | - Youjun Zhang
- State Key Laboratory of Vegetable BiobreedingDepartment of Plant ProtectionInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
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Chen CY, Shao Z, Wang G, Zhao B, Hardtke HA, Leong J, Zhou T, Zhang YJ, Qiao H. Histone acetyltransferase HAF2 associates with PDC to control H3K14ac and H3K23ac in ethylene response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573642. [PMID: 38260516 PMCID: PMC10802238 DOI: 10.1101/2023.12.31.573642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Ethylene plays its essential roles in plant development, growth, and defense responses by controlling the transcriptional reprogramming, in which EIN2-C-directed regulation of histone acetylation is the first key-step for chromatin to perceive ethylene signaling. However, the histone acetyltransferase in this process remains unknown. Here, we identified histone acetyltransferase HAF2, and mutations in HAF2 confer plants with ethylene insensitivity. Furthermore, we found that HAF2 interacts with EIN2-C in response to ethylene. Biochemical assays demonstrated that the bromodomain of HAF2 binds to H3K14ac and H3K23ac peptides with a distinct affinity for H3K14ac; the HAT domain possesses acetyltransferase catalytic activity for H3K14 and H3K23 acetylation, with a preference for H3K14. ChIP-seq results provide additional evidence supporting the role of HAF2 in regulating H3K14ac and H3K23ac levels in response to ethylene. Finally, our findings revealed that HAF2 co-functions with pyruvate dehydrogenase complex (PDC) to regulate H3K14ac and H3K23ac in response to ethylene in an EIN2 dependent manner. Overall, this research reveals that HAF2 as a histone acetyltransferase that forms a complex with EIN2-C and PDC, collectively governing histone acetylation of H3H14ac and H3K23ac, preferentially for H3K14 in response to ethylene.
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Yin J, Ren W, Fry EL, Sun S, Han H, Guo F. DNA methylation mediates overgrazing-induced clonal transgenerational plasticity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165338. [PMID: 37414175 DOI: 10.1016/j.scitotenv.2023.165338] [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: 04/23/2023] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Overgrazing generally induces dwarfism in grassland plants, and these phenotypic traits could be transmitted to clonal offspring even when overgrazing is excluded. However, the dwarfism-transmitted mechanism remains largely unknown, despite generally thought to be enabled by epigenetic modification. To clarify the potential role of DNA methylation on clonal transgenerational effects, we conducted a greenhouse experiment with Leymus chinensis clonal offspring from different cattle/sheep overgrazing histories via the demethylating agent 5-azacytidine. The results showed that clonal offspring from overgrazed (by cattle or sheep) parents were dwarfed and the auxin content of leaves significantly decreased compared to offspring from no-grazed parents'. The 5-azaC application generally increased the auxin content and promoted the growth of overgrazed offspring while inhibited no-grazed offspring growth. Meanwhile, there were similar trends in the expression level of genes related to auxin-responsive target genes (ARF7, ARF19), and signal transduction gene (AZF2). These results suggest that DNA methylation leads to overgrazing-induced plant transgenerational dwarfism via inhibiting auxin signal pathway.
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Affiliation(s)
- Jingjing Yin
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Weibo Ren
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China; Key Laboratory of Forage Breeding and Seed Production of Inner Mongolia, Inner Mongolia M-Grass Ecology and Environment (Group) Co., Ltd., Hohhot 010016, China.
| | - Ellen L Fry
- Department of Biology, Edge Hill University, Ormskirk, Lancashire L39 4QP, UK
| | - Siyuan Sun
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Huijie Han
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Fenghui Guo
- Industrial Crop Institute, Shanxi Agricultural University, Taiyuan, China
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Meijer A, Atighi MR, Demeestere K, De Meyer T, Vandepoele K, Kyndt T. Dicer-like 3a mediates intergenerational resistance against root-knot nematodes in rice via hormone responses. PLANT PHYSIOLOGY 2023; 193:2071-2085. [PMID: 37052181 DOI: 10.1093/plphys/kiad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
In a continuously changing and challenging environment, passing down the memory of encountered stress factors to offspring could provide an evolutionary advantage. In this study, we demonstrate the existence of "intergenerational acquired resistance" in the progeny of rice (Oryza sativa) plants attacked by the belowground parasitic nematode Meloidogyne graminicola. Transcriptome analyses revealed that genes involved in defense pathways are generally downregulated in progeny of nematode-infected plants under uninfected conditions but show a stronger induction upon nematode infection. This phenomenon was termed "spring loading" and depends on initial downregulation by the 24-nucleotide (nt) siRNA biogenesis gene dicer-like 3a (dcl3a) involved in the RNA-directed DNA methylation pathway. Knockdown of dcl3a led to increased nematode susceptibility and abolished intergenerational acquired resistance, as well as jasmonic acid/ethylene spring loading in the offspring of infected plants. The importance of ethylene signaling in intergenerational resistance was confirmed by experiments on a knockdown line of ethylene insensitive 2 (ein2b), which lacks intergenerational acquired resistance. Taken together, these data indicate a role for DCL3a in regulating plant defense pathways during both within-generation and intergenerational resistance against nematodes in rice.
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Affiliation(s)
- Anikó Meijer
- Department of Biotechnology, Ghent University, Ghent 9000, Belgium
| | - Mohammad Reza Atighi
- Department of Biotechnology, Ghent University, Ghent 9000, Belgium
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, PO Box 14115-336 Tehran, Iran
| | - Kristof Demeestere
- Department of Green Chemistry and Technology, Research group EnVOC, Ghent University, Ghent 9000, Belgium
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent 9000, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent 9052, Belgium
| | - Tina Kyndt
- Department of Biotechnology, Ghent University, Ghent 9000, Belgium
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Solanki M, Shukla LI. Recent advances in auxin biosynthesis and homeostasis. 3 Biotech 2023; 13:290. [PMID: 37547917 PMCID: PMC10400529 DOI: 10.1007/s13205-023-03709-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 07/18/2023] [Indexed: 08/08/2023] Open
Abstract
The plant proliferation is linked with auxins which in turn play a pivotal role in the rate of growth. Also, auxin concentrations could provide insights into the age, stress, and events leading to flowering and fruiting in the sessile plant kingdom. The role in rejuvenation and plasticity is now evidenced. Interest in plant auxins spans many decades, information from different plant families for auxin concentrations, transcriptional, and epigenetic evidences for gene regulation is evaluated here, for getting an insight into pattern of auxin biosynthesis. This biosynthesis takes place via an tryptophan-independent and tryptophan-dependent pathway. The independent pathway initiated before the tryptophan (trp) production involves indole as the primary substrate. On the other hand, the trp-dependent IAA pathway passes through the indole pyruvic acid (IPyA), indole-3-acetaldoxime (IAOx), and indole acetamide (IAM) pathways. Investigations on trp-dependent pathways involved mutants, namely yucca (1-11), taa1, nit1, cyp79b and cyp79b2, vt2 and crd, and independent mutants of tryptophan, ins are compiled here. The auxin conjugates of the IAA amide and ester-linked mutant gh3, iar, ilr, ill, iamt1, ugt, and dao are remarkable and could facilitate the assimilation of auxins. Efforts are made herein to provide an up-to-date detailed information about biosynthesis leading to plant sustenance. The vast information about auxin biosynthesis and homeostasis is consolidated in this review with a simplified model of auxin biosynthesis with keys and clues for important missing links since auxins can enable the plants to proliferate and override the environmental influence and needs to be probed for applications in sustainable agriculture. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03709-6.
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Affiliation(s)
- Manish Solanki
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, 605014 India
- Puducherry, India
| | - Lata Israni Shukla
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, 605014 India
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Liu D, Yan G, Wang S, Yu L, Lin W, Lu S, Guo L, Yang QY, Dai C. Comparative transcriptome profiling reveals the multiple levels of crosstalk in phytohormone networks in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37154465 PMCID: PMC10363766 DOI: 10.1111/pbi.14063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/13/2023] [Accepted: 04/12/2023] [Indexed: 05/10/2023]
Abstract
Plant hormones are the intrinsic factors that control plant development. The integration of different phytohormone pathways in a complex network of synergistic, antagonistic and additive interactions has been elucidated in model plants. However, the systemic level of transcriptional responses to hormone crosstalk in Brassica napus is largely unknown. Here, we present an in-depth temporal-resolution study of the transcriptomes of the seven hormones in B. napus seedlings. Differentially expressed gene analysis revealed few common target genes that co-regulated (up- and down-regulated) by seven hormones; instead, different hormones appear to regulate distinct members of protein families. We then constructed the regulatory networks between the seven hormones side by side, which allowed us to identify key genes and transcription factors that regulate the hormone crosstalk in B. napus. Using this dataset, we uncovered a novel crosstalk between gibberellin and cytokinin in which cytokinin homeostasis was mediated by RGA-related CKXs expression. Moreover, the modulation of gibberellin metabolism by the identified key transcription factors was confirmed in B. napus. Furthermore, all data were available online from http://yanglab.hzau.edu.cn/BnTIR/hormone. Our study reveals an integrated hormone crosstalk network in Brassica napus, which also provides a versatile resource for future hormone studies in plant species.
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Affiliation(s)
- Dongxu Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Guanbo Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Shengbo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Liangqian Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wei Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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Jiang K, Guo H, Zhai J. Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:381-398. [PMID: 36223083 DOI: 10.1111/jipb.13384] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Both phytohormone signaling and epigenetic mechanisms have long been known to play crucial roles in plant development and plasticity in response to ambient stimuli. Indeed, diverse signaling pathways mediated by phytohormones and epigenetic processes integrate multiple upstream signals to regulate various plant traits. Emerging evidence indicates that phytohormones and epigenetic processes interact at multiple levels. In this review, we summarize the current knowledge of the interplay between phytohormones and epigenetic processes from the perspective of phytohormone biology. We also review chemical regulators used in epigenetic studies and propose strategies for developing novel regulators using multidisciplinary approaches.
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Affiliation(s)
- Kai Jiang
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
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Liang Y, Heyman J, Lu R, De Veylder L. Evolution of wound-activated regeneration pathways in the plant kingdom. Eur J Cell Biol 2023; 102:151291. [PMID: 36709604 DOI: 10.1016/j.ejcb.2023.151291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Regeneration serves as a self-protective mechanism that allows a tissue or organ to recover its entire form and function after suffering damage. However, the regenerative capacity varies greatly within the plant kingdom. Primitive plants frequently display an amazing regenerative ability as they have developed a complex system and strategy for long-term survival under extreme stress conditions. The regenerative ability of dicot species is highly variable, but that of monocots often exhibits extreme recalcitrance to tissue replenishment. Recent studies have revealed key factors and signals that affect cell fate during plant regeneration, some of which are conserved among the plant lineage. Among these, several members of the ETHYLENE RESPONSE FACTOR (ERF) transcription factors have been implicated in wound signaling, playing crucial roles in the regenerative mechanisms after different types of wounding. An understanding of plant regeneration may ultimately lead to an increased regenerative potential of recalcitrant species, producing more high-yielding, multi-resistant and environmentally friendly crops and ensuring the long-term development of global agriculture.
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Affiliation(s)
- Yuanke Liang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Ran Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium.
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11
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Jia H, Zuo Q, Sadeghnezhad E, Zheng T, Chen X, Dong T, Fang J. HDAC19 recruits ERF4 to the MYB5a promoter and diminishes anthocyanin accumulation during grape ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:127-144. [PMID: 36423230 DOI: 10.1111/tpj.16040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
DNA acetylation alters the expression of responsive genes during plant development. In grapes (Vitis vinifera), however, little is known about this regulatory mechanism. In the present study, 'Kyoho' grapes treated with trichostatin A (TSA, a deacetylase inhibitor) were used for transcriptome sequencing and quantitative proteomics analysis. We observed that acetylation was associated with anthocyanin accumulation and gene expression. Acetylation positively regulated phenylalanine metabolism and flavonoid biosynthesis pathways. Using omics analysis, we detected an increase in the levels of the AP2/EREBP transcription factor family after TSA treatment, indicating its association with acetylation-deacetylation dynamics in grapes. Furthermore, ethylene response factor 4 (ERF4) physically interacted with VvHDAC19, a histone deacetylase, which synergistically reduced the expression of target genes involved in anthocyanin biosynthesis owing to the binding of VvERF4 to the GCC-box cis-regulatory element in the VvMYB5a promoter. VvHDAC19 and VvERF4 also controlled anthocyanin biosynthesis and accumulation by regulating acetylation levels of histones H3 and H4. Therefore, alterations in histone modification can significantly regulate the expression of genes involved in anthocyanin biosynthesis and affect grape ripening.
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Affiliation(s)
- Haifeng Jia
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
- NJAU (Suqian) Academy of Protected Horticultures, Suqian, China
| | - Qianqian Zuo
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ehsan Sadeghnezhad
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ting Zheng
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Xueqin Chen
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Tianyu Dong
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - JinggGui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
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12
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Yang Q, Wu X, Gao Y, Ni J, Li J, Pei Z, Bai S, Teng Y. PpyABF3 recruits the COMPASS-like complex to regulate bud dormancy maintenance via integrating ABA signaling and GA catabolism. THE NEW PHYTOLOGIST 2023; 237:192-203. [PMID: 36151925 DOI: 10.1111/nph.18508] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Bud dormancy is essential for perennial trees that survive the cold winters and to flower on time in the following spring. Histone modifications have been reported to be involved in the control of the dormancy cycle and DAM/SVPs are considered targets. However, how the histone modification marks are added to the specific gene loci during bud dormancy cycle is still unknown. Using yeast-two hybrid library screening and co-immunoprecipitation assays, we found that PpyABF3, a key protein regulating bud dormancy, recruits Complex of Proteins Associated with Set1-like complex via interacting with PpyWDR5a, which increases the H3K4me3 deposition at DAM4 locus. Chromatin immunoprecipitation-quantitative polymerase chain reaction showed that PpyGA2OX1 was downstream gene of PpyABF3 and it was also activated by H3K4me3 deposition. Silencing of GA2OX1 in pear calli and pear buds resulted in a similar phenotype with silencing of ABF3. Furthermore, overexpression of PpyWDR5a increased H3K4me3 levels at DAM4 and GA2OX1 loci and inhibited the growth of pear calli, whereas silencing of PpyWDR5a in pear buds resulted in a higher bud-break percentage. Our findings provide new insights into how H3K4me3 marks are added to dormancy-related genes in perennial woody plants and reveal a novel mechanism by which ABF3 integrates abscisic acid signaling and gibberellic acid catabolism during bud dormancy maintenance.
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Affiliation(s)
- Qinsong Yang
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xinyue Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yuhao Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Junbei Ni
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jinjin Li
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Ziqi Pei
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Songling Bai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yuanwen Teng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, 572000, China
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13
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Ding Y, Zou LH, Wu J, Ramakrishnan M, Gao Y, Zhao L, Zhou M. The pattern of DNA methylation alteration, and its association with the expression changes of non-coding RNAs and mRNAs in Moso bamboo under abiotic stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111451. [PMID: 36075278 DOI: 10.1016/j.plantsci.2022.111451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/01/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Epigenetic changes play an important role in plant growth and development and in stress response. However, DNA methylation pattern and its relationship with the expression changes of non-coding RNAs and mRNAs of Moso bamboo in response to abiotic stress is still largely unknown. In this work, we used whole-genome bisulfite sequencing in combination with whole-transcriptome sequencing to analyze the DNA methylation and transcription patterns of mRNAs and non-coding RNAs in Moso bamboo under abiotic stresses such as cold, heat, ultraviolet (UV) and salinity. We found that CHH methylation in the promoter region was positively correlated with gene expression, while CHG and CHH methylations in the gene body regions were negatively associated with gene expression. Moreover, CG and CHG methylations in the promoter regions were negatively correlated with the transcript abundance of long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and circular RNAs (circRNAs). Similarly, the methylation levels of three contexts in the genic regions were negatively correlated with the transcript abundance of lncRNAs and miRNAs but positively correlated with that of circRNAs. In addition, we suggested that the reduction of 21-nt and 24-nt small interfering RNA (siRNA) expression tended to increase methylation levels in the genic regions. We found that stress-responsive genes such as CRPK1, HSFB2A and CIPK were differentially methylated and expressed. Our results also proposed that DNA methylation may regulate the expression of the transcription factors (TFs) and plant hormone signalling genes such as IAA9, MYC2 and ERF110 in response to abiotic stress. This study firstly reports the abiotic stress-responsive DNA methylation pattern and its involvement of expression of coding RNAs and non-coding RNAs in Moso bamboo. The results expand the knowledge of epigenetic mechanisms in Moso bamboo under abiotic stress and support in-depth deciphering of the function of specific non-coding RNAs in future studies.
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Affiliation(s)
- Yiqian Ding
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Long-Hai Zou
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
| | - Jiajun Wu
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Muthusamy Ramakrishnan
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Yubang Gao
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Liangzhen Zhao
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingbing Zhou
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
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14
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Nguyen NH, Vu NT, Cheong JJ. Transcriptional Stress Memory and Transgenerational Inheritance of Drought Tolerance in Plants. Int J Mol Sci 2022; 23:12918. [PMID: 36361708 PMCID: PMC9654142 DOI: 10.3390/ijms232112918] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 12/03/2023] Open
Abstract
Plants respond to drought stress by producing abscisic acid, a chemical messenger that regulates gene expression and thereby expedites various physiological and cellular processes including the stomatal operation to mitigate stress and promote tolerance. To trigger or suppress gene transcription under drought stress conditions, the surrounding chromatin architecture must be converted between a repressive and active state by epigenetic remodeling, which is achieved by the dynamic interplay among DNA methylation, histone modifications, loop formation, and non-coding RNA generation. Plants can memorize chromatin status under drought conditions to enable them to deal with recurrent stress. Furthermore, drought tolerance acquired during plant growth can be transmitted to the next generation. The epigenetically modified chromatin architectures of memory genes under stressful conditions can be transmitted to newly developed cells by mitotic cell division, and to germline cells of offspring by overcoming the restraints on meiosis. In mammalian cells, the acquired memory state is completely erased and reset during meiosis. The mechanism by which plant cells overcome this resetting during meiosis to transmit memory is unclear. In this article, we review recent findings on the mechanism underlying transcriptional stress memory and the transgenerational inheritance of drought tolerance in plants.
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Affiliation(s)
- Nguyen Hoai Nguyen
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City 700000, Vietnam
| | - Nam Tuan Vu
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
| | - Jong-Joo Cheong
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
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15
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Ni ZQ, Jin J, Ye Y, Luo WW, Zheng YN, Tong ZK, Lv YQ, Ye JH, Wu LY. Integrative Transcriptomic and Phytohormonal Analyses Provide Insights into the Cold Injury Recovery Mechanisms of Tea Leaves. PLANTS (BASEL, SWITZERLAND) 2022; 11:2751. [PMID: 36297775 PMCID: PMC9610371 DOI: 10.3390/plants11202751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/10/2022] [Accepted: 06/20/2022] [Indexed: 06/16/2023]
Abstract
Tea plant is susceptible to low temperature, while the cold injury recovery mechanisms of tea leaves are still unclear. Windbreak has an effective and gradient range of protecting tea plants. Tea plants with increasing cold damage degree have varying recovery status accordingly, which are the ideal objects for investigating the cold injury recovery mechanisms of tea leaves. Here, we investigated the transcriptome and phytohormone profiles of tea leaves with different cold injury degrees in recovery (adjacent to the windbreak), and the levels of chlorophylls, malondialdehyde, major phytohormones as well as the activities of peroxidase (POD) and superoxide dismutase (SOD) were also measured. The results showed the content of total chlorophylls and the activity of POD in mature tea leaves gradually decreased with the distance to windbreak, while SOD showed the opposite. The major phytohormones were highly accumulated in the moderately cold-injured tea leaves. The biosynthesis of abscisic acid (ABA) was enhanced in the moderate cold damaged tea leaves, suggesting that ABA plays an important role in the cold response and resistance of tea plants. The transcriptomic result showed that the samples in different rows were well discriminated, and the pathways of plant-pathogen interaction and flavonoid biosynthesis were enriched based on KEGG analysis. WRKY, GRAS and NAC were the top classes of transcription factors differentially expressed in the different cold-injured tea leaves. Thus, windbreak is effective to protect adjacent tea plants from cold wave, and phytohormones importantly participate in the cold injury recovery of tea leaves.
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Affiliation(s)
- Zhi-Qi Ni
- Tea Research Institute, Zijingang Campus, Zhejiang University, Hangzhou 310013, China
| | - Jing Jin
- Zhejiang Agricultural Technical Extension Center, 29 Fengqi East Road, Hangzhou 310020, China
| | - Ying Ye
- Tea Research Institute, Zijingang Campus, Zhejiang University, Hangzhou 310013, China
| | - Wen-Wen Luo
- Jinhua Department of Economic Specialty Technology Promotion, 828 Shuanglong South Road, Jinhua 321000, China
| | - Ya-Nan Zheng
- Jinhua Department of Economic Specialty Technology Promotion, 828 Shuanglong South Road, Jinhua 321000, China
| | - Zheng-Kun Tong
- Lanxi Chishan Lake Green Farm Co., Ltd., Lanxi 321100, China
| | - Yi-Qing Lv
- Tea Research Institute, Zijingang Campus, Zhejiang University, Hangzhou 310013, China
| | - Jian-Hui Ye
- Tea Research Institute, Zijingang Campus, Zhejiang University, Hangzhou 310013, China
| | - Liang-Yu Wu
- College of Horticulture, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou 350002, China
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16
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Zhan C, Shen S, Yang C, Liu Z, Fernie AR, Graham IA, Luo J. Plant metabolic gene clusters in the multi-omics era. TRENDS IN PLANT SCIENCE 2022; 27:981-1001. [PMID: 35365433 DOI: 10.1016/j.tplants.2022.03.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Secondary metabolism in plants gives rise to a vast array of small-molecule natural products. The discovery of operon-like gene clusters in plants has provided a new perspective on the evolution of specialized metabolism and the opportunity to rapidly advance the metabolic engineering of natural product production. Here, we review historical aspects of the study of plant metabolic gene clusters as well as general strategies for identifying plant metabolic gene clusters in the multi-omics era. We also emphasize the exploration of their natural variation and evolution, as well as new strategies for the prospecting of plant metabolic gene clusters and a deeper understanding of how their structure influences their function.
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Affiliation(s)
- Chuansong Zhan
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Shuangqian Shen
- College of Tropical Crops, Hainan University, Haikou 570228, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Alisdair R Fernie
- Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Ian A Graham
- Center for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
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17
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Aizezi Y, Xie Y, Guo H, Jiang K. New Wine in an Old Bottle: Utilizing Chemical Genetics to Dissect Apical Hook Development. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081285. [PMID: 36013464 PMCID: PMC9410295 DOI: 10.3390/life12081285] [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: 07/14/2022] [Revised: 08/12/2022] [Accepted: 08/17/2022] [Indexed: 02/08/2023]
Abstract
The apical hook is formed by dicot seedlings to protect the tender shoot apical meristem during soil emergence. Regulated by many phytohormones, the apical hook has been taken as a model to study the crosstalk between individual signaling pathways. Over recent decades, the roles of different phytohormones and environmental signals in apical hook development have been illustrated. However, key regulators downstream of canonical hormone signaling have rarely been identified via classical genetics screening, possibly due to genetic redundancy and/or lethal mutation. Chemical genetics that utilize small molecules to perturb and elucidate biological processes could provide a complementary strategy to overcome the limitations in classical genetics. In this review, we summarize current progress in hormonal regulation of the apical hook, and previously reported chemical tools that could assist the understanding of this complex developmental process. We also provide insight into novel strategies for chemical screening and target identification, which could possibly lead to discoveries of new regulatory components in apical hook development, or unidentified signaling crosstalk that is overlooked by classical genetics screening.
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Affiliation(s)
- Yalikunjiang Aizezi
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yinpeng Xie
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
- Correspondence: (H.G.); (K.J.)
| | - Kai Jiang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
- Correspondence: (H.G.); (K.J.)
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18
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Govender P, Ghai M, Okpeku M. Sex-specific DNA methylation: impact on human health and development. Mol Genet Genomics 2022; 297:1451-1466. [PMID: 35969270 DOI: 10.1007/s00438-022-01935-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
Abstract
Human evolution has shaped gender differences between males and females. Over the years, scientific studies have proposed that epigenetic modifications significantly influence sex-specific differences. The evolution of sex chromosomes with epigenetics as the driving force may have led to one sex being more adaptable than the other when exposed to various factors over time. Identifying and understanding sex-specific differences, particularly in DNA methylation, will help determine how each gender responds to factors, such as disease susceptibility, environmental exposure, brain development and neurodegeneration. From a medicine and health standpoint, sex-specific methylation studies have shed light on human disease severity, progression, and response to therapeutic intervention. Interesting findings in gender incongruent individuals highlight the role of genetic makeup in influencing DNA methylation differences. Sex-specific DNA methylation studies will empower the biotechnology and pharmaceutical industry with more knowledge to identify biomarkers, design and develop sex bias drugs leading to better treatment in men and women based on their response to different diseases.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
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19
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Wang JL, Di DW, Luo P, Zhang L, Li XF, Guo GQ, Wu L. The roles of epigenetic modifications in the regulation of auxin biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:959053. [PMID: 36017262 PMCID: PMC9396225 DOI: 10.3389/fpls.2022.959053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/15/2022] [Indexed: 06/01/2023]
Abstract
Auxin is one of the most important plant growth regulators of plant morphogenesis and response to environmental stimuli. Although the biosynthesis pathway of auxin has been elucidated, the mechanisms regulating auxin biosynthesis remain poorly understood. The transcription of auxin biosynthetic genes is precisely regulated by complex signaling pathways. When the genes are expressed, epigenetic modifications guide mRNA synthesis and therefore determine protein production. Recent studies have shown that different epigenetic factors affect the transcription of auxin biosynthetic genes. In this review, we focus our attention on the molecular mechanisms through which epigenetic modifications regulate auxin biosynthesis.
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Affiliation(s)
- Jun-Li Wang
- Ministry of Education (MOE) Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dong-Wei Di
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Pan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Li Zhang
- Basic Forestry and Proteomics Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiao-Feng Li
- Ministry of Education (MOE) Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guang-Qin Guo
- Ministry of Education (MOE) Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lei Wu
- Ministry of Education (MOE) Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou, China
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20
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Villagómez-Aranda AL, Feregrino-Pérez AA, García-Ortega LF, González-Chavira MM, Torres-Pacheco I, Guevara-González RG. Activating stress memory: eustressors as potential tools for plant breeding. PLANT CELL REPORTS 2022; 41:1481-1498. [PMID: 35305133 PMCID: PMC8933762 DOI: 10.1007/s00299-022-02858-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/26/2022] [Indexed: 05/08/2023]
Abstract
Plants are continuously exposed to stress conditions, such that they have developed sophisticated and elegant survival strategies, which are reflected in their phenotypic plasticity, priming capacity, and memory acquisition. Epigenetic mechanisms play a critical role in modulating gene expression and stress responses, allowing malleability, reversibility, stability, and heritability of favourable phenotypes to enhance plant performance. Considering the urgency to improve our agricultural system because of going impacting climate change, potential and sustainable strategies rely on the controlled use of eustressors, enhancing desired characteristics and yield and shaping stress tolerance in crops. However, for plant breeding purposes is necessary to focus on the use of eustressors capable of establishing stable epigenetic marks to generate a transgenerational memory to stimulate a priming state in plants to face the changing environment.
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Affiliation(s)
- A L Villagómez-Aranda
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - A A Feregrino-Pérez
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - L F García-Ortega
- Laboratory of Learning and Research in Biological Computing, Centre for Research and Advanced Studies, National Polytechnic Institute (CINVESTAV), Irapuato, Guanajuato, Mexico
| | - M M González-Chavira
- Molecular Markers Laboratory, Bajío Experimental Field, National Institute for Forestry, Agriculture and Livestock Research (INIFAP), Celaya-San Miguel de Allende, Celaya, Guanajuato, Mexico
| | - I Torres-Pacheco
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - R G Guevara-González
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico.
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21
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Aziz U, Rehmani MS, Wang L, Xian B, Luo X, Shu K. Repressors: the gatekeepers of phytohormone signaling cascades. PLANT CELL REPORTS 2022; 41:1333-1341. [PMID: 35262769 DOI: 10.1007/s00299-022-02853-2] [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: 12/05/2021] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Coordinated phytohormone signal transduction, in which repressors are the key players, is essential to balance plant development and stress response. In the absence of phytohormones, repressors interplay to terminate the transcription of phytohormone-responsive genes. For phytohormone signal transduction, degradation or inactivation of the repressors is a prerequisite, a process in which proteasomal degradation or protein modifications, such as phosphorylation, are involved. In this review, we summarize the various repressor proteins and their methods of regulation. In addition, we also shed light on other post-transcriptional modifications, including protein sumoylation, acetylation, methylation, and S-nitrosylation, which might be involved in repressor regulation. We conclude that repressors are the gatekeepers of phytohormone signaling, allowing transcription of phytohormone-responsive genes only when required and thus serving as a universal mechanism to conserve energy in plants. Finally, we strongly recommend that plant research should be focused further on elucidating the mechanisms regulating repressor abundance or activity, to improve our understanding of phytohormone signal transduction.
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Affiliation(s)
- Usman Aziz
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China
| | - Muhammad Saad Rehmani
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China
| | - Lei Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China
| | - Baoshan Xian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China
| | - Xiaofeng Luo
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China
| | - Kai Shu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China.
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China.
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22
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Hao Z, Ma S, Liang L, Feng T, Xiong M, Lian S, Zhu J, Chen Y, Meng L, Li M. Candidate Genes and Pathways in Rice Co-Responding to Drought and Salt Identified by gcHap Network. Int J Mol Sci 2022; 23:ijms23074016. [PMID: 35409377 PMCID: PMC8999833 DOI: 10.3390/ijms23074016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/26/2022] [Accepted: 04/01/2022] [Indexed: 01/24/2023] Open
Abstract
Drought and salinity stresses are significant abiotic factors that limit rice yield. Exploring the co-response mechanism to drought and salt stress will be conducive to future rice breeding. A total of 1748 drought and salt co-responsive genes were screened, most of which are enriched in plant hormone signal transduction, protein processing in the endoplasmic reticulum, and the MAPK signaling pathways. We performed gene-coding sequence haplotype (gcHap) network analysis on nine important genes out of the total amount, which showed significant differences between the Xian/indica and Geng/japonica population. These genes were combined with related pathways, resulting in an interesting mechanistic draft called the ‘gcHap-network pathway’. Meanwhile, we collected a lot of drought and salt breeding varieties, especially the introgression lines (ILs) with HHZ as the parent, which contained the above-mentioned nine genes. This might imply that these ILs have the potential to improve the tolerance to drought and salt. In this paper, we focus on the relationship of drought and salt co-response gene gcHaps and their related pathways using a novel angle. The haplotype network will be helpful to explore the desired haplotypes that can be implemented in haplotype-based breeding programs.
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Affiliation(s)
- Zhiqi Hao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sai Ma
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lunping Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Ting Feng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Mengyuan Xiong
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Shangshu Lian
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jingyan Zhu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Yanjun Chen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lijun Meng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Correspondence: (L.M.); (M.L.)
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Correspondence: (L.M.); (M.L.)
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23
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Brenya E, Pervin M, Chen ZH, Tissue DT, Johnson S, Braam J, Cazzonelli CI. Mechanical stress acclimation in plants: Linking hormones and somatic memory to thigmomorphogenesis. PLANT, CELL & ENVIRONMENT 2022; 45:989-1010. [PMID: 34984703 DOI: 10.1111/pce.14252] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
A single event of mechanical stimulation is perceived by mechanoreceptors that transduce rapid transient signalling to regulate gene expression. Prolonged mechanical stress for days to weeks culminates in cellular changes that strengthen the plant architecture leading to thigmomorphogenesis. The convergence of multiple signalling pathways regulates mechanically induced tolerance to numerous biotic and abiotic stresses. Emerging evidence showed prolonged mechanical stimulation can modify the baseline level of gene expression in naive tissues, heighten gene expression, and prime disease resistance upon a subsequent pathogen encounter. The phenotypes of thigmomorphogenesis can persist throughout growth without continued stimulation, revealing somatic-stress memory. Epigenetic processes regulate TOUCH gene expression and could program transcriptional memory in differentiating cells to program thigmomorphogenesis. We discuss the early perception, gene regulatory and phytohormone pathways that facilitate thigmomorphogenesis and mechanical stress acclimation in Arabidopsis and other plant species. We provide insights regarding: (1) the regulatory mechanisms induced by single or prolonged events of mechanical stress, (2) how mechanical stress confers transcriptional memory to induce cross-acclimation to future stress, and (3) why thigmomorphogenesis might resemble an epigenetic phenomenon. Deeper knowledge of how prolonged mechanical stimulation programs somatic memory and primes defence acclimation could transform solutions to improve agricultural sustainability in stressful environments.
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Affiliation(s)
- Eric Brenya
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Mahfuza Pervin
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Zhong-Hua Chen
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
- School of Science, Western Sydney University, Richmond, New South Wales, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Scott Johnson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Janet Braam
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Christopher I Cazzonelli
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
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24
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Iwase A, Takebayashi A, Aoi Y, Favero DS, Watanabe S, Seo M, Kasahara H, Sugimoto K. 4-Phenylbutyric acid promotes plant regeneration as an auxin by being converted to phenylacetic acid via an IBR3-independent pathway. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:51-58. [PMID: 35601015 PMCID: PMC9080989 DOI: 10.5511/plantbiotechnology.21.1224b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/24/2021] [Indexed: 05/07/2023]
Abstract
4-Phenylbutyric acid (4PBA) is utilized as a drug to treat urea cycle disorders and is also being studied as a potential anticancer drug that acts via its histone deacetylase (HDAC) inhibitor activity. During a search to find small molecules that affect plant regeneration in Arabidopsis, we found that 4PBA treatment promotes this process by mimicking the effect of exogenous auxin. Specifically, plant tissue culture experiments revealed that a medium containing 4PBA enhances callus formation and subsequent shoot regeneration. Analyses with auxin-responsive or cytokinin-responsive marker lines demonstrated that 4PBA specifically enhances AUXIN RESPONSE FACTOR (ARF)-dependent auxin responses. Our western blot analyses showed that 4PBA treatment does not enhance histone acetylation in Arabidopsis, in contrast to butyric acid and trichostatin A, other chemicals often used as HDAC inhibitors, suggesting this mechanism of action does not explain the observed effect of 4PBA on regeneration. Finally, mass spectroscopic analysis and genetic approaches uncovered that 4PBA in Arabidopsis plants is converted to phenylacetic acid (PAA), a known natural auxin, in a manner independent of peroxisomal IBR3-related β-oxidation. This study demonstrates that 4PBA application promotes regeneration in explants via its auxin activity and has potential applications to not only plant tissue culture engineering but also research on the plant β-oxidation pathway.
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Affiliation(s)
- Akira Iwase
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
- E-mail: Tel: +81-45-503-9570 Fax: +81-45-503-9591
| | - Arika Takebayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki Aoi
- Department of Biological Production Science, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - David S Favero
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Shunsuke Watanabe
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Kasahara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- E-mail: Tel: +81-45-503-9570 Fax: +81-45-503-9591
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25
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Plant Growth Regulators in Tree Rooting. PLANTS 2022; 11:plants11060805. [PMID: 35336687 PMCID: PMC8949883 DOI: 10.3390/plants11060805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022]
Abstract
Trees are long-lived organisms with complex life cycles that provide enormous benefits both in natural and cultivated stands [...]
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26
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Interactions of Gibberellins with Phytohormones and Their Role in Stress Responses. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8030241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Gibberellins are amongst the main plant growth regulators. Discovered over a century ago, the interest in gibberellins research is growing due to their current and potential applications in crop production and their role in the responses to environmental stresses. In the present review, the current knowledge on gibberellins’ homeostasis and modes of action is outlined. Besides this, the complex interrelations between gibberellins and other plant growth regulators are also described, providing an intricate network of interactions that ultimately drives towards precise and specific gene expression. Thus, genes and proteins identified as being involved in gibberellin responses in model and non-model species are highlighted. Furthermore, the molecular mechanisms governing the gibberellins’ relation to stress responses are also depicted. This review aims to provide a comprehensive picture of the state-of-the-art of the current perceptions of the interactions of gibberellins with other phytohormones, and their responses to plant stresses, thus allowing for the identification of the specific mechanisms involved. This knowledge will help us to improve our understanding of gibberellins’ biology, and might help increase the biotechnological toolbox needed to refine plant resilience, particularly under a climate change scenario.
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27
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Alejo-Vinogradova MT, Ornelas-Ayala D, Vega-León R, Garay-Arroyo A, García-Ponce B, R Álvarez-Buylla E, Sanchez MDLP. Unraveling the role of epigenetic regulation in asymmetric cell division during plant development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:38-49. [PMID: 34518884 DOI: 10.1093/jxb/erab421] [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: 05/11/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
Asymmetric cell divisions are essential to generate different cellular lineages. In plants, asymmetric cell divisions regulate the correct formation of the embryo, stomatal cells, apical and root meristems, and lateral roots. Current knowledge of regulation of asymmetric cell divisions suggests that, in addition to the function of key transcription factor networks, epigenetic mechanisms play crucial roles. Therefore, we highlight the importance of epigenetic regulation and chromatin dynamics for integration of signals and specification of cells that undergo asymmetric cell divisions, as well as for cell maintenance and cell fate establishment of both progenitor and daughter cells. We also discuss the polarization and segregation of cell components to ensure correct epigenetic memory or resetting of epigenetic marks during asymmetric cell divisions.
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Affiliation(s)
- M Teresa Alejo-Vinogradova
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - Diego Ornelas-Ayala
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - Rosario Vega-León
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - María de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
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Sun C, Li D, Gao Z, Gao L, Shang L, Wang M, Qiao J, Ding S, Li C, Geisler M, Jiang D, Qi Y, Qian Q. OsRLR4 binds to the OsAUX1 promoter to negatively regulate primary root development in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:118-134. [PMID: 34726825 DOI: 10.1111/jipb.13183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Root architecture is one of the most important agronomic traits that determines rice crop yield. The primary root (PR) absorbs mineral nutrients and provides mechanical support; however, the molecular mechanisms of PR elongation remain unclear in rice. Here, the two loss-of-function T-DNA insertion mutants of root length regulator 4 (OsRLR4), osrlr4-1 and osrlr4-2 with longer PR, and three OsRLR4 overexpression lines, OE-OsRLR4-1/-2/-3 with shorter PR compared to the wild type/Hwayoung (WT/HY), were identified. OsRLR4 is one of five members of the PRAF subfamily of the regulator chromosome condensation 1 (RCC1) family. Phylogenetic analysis of OsRLR4 from wild and cultivated rice indicated that it is under selective sweeps, suggesting its potential role in domestication. OsRLR4 controls PR development by regulating auxin accumulation in the PR tip and thus the root apical meristem activity. A series of biochemical and genetic analyses demonstrated that OsRLR4 functions directly upstream of the auxin transporter OsAUX1. Moreover, OsRLR4 interacts with the TRITHORAX-like protein OsTrx1 to promote H3K4me3 deposition at the OsAUX1 promoter, thus altering its transcription level. This work provides insight into the cooperation of auxin and epigenetic modifications in regulating root architecture and provides a genetic resource for plant architecture breeding.
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Affiliation(s)
- Chendong Sun
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Lin'an Hangzhou, 311300, China
| | - Dongming Li
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Lei Gao
- College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, Shenzhen, China
| | - Lianguang Shang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Mei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiyue Qiao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shilin Ding
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, CH-1700, Switzerland
| | - Dean Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanhua Qi
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
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29
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Mishra BS, Sharma M, Laxmi A. Role of sugar and auxin crosstalk in plant growth and development. PHYSIOLOGIA PLANTARUM 2022; 174:e13546. [PMID: 34480799 DOI: 10.1111/ppl.13546] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 05/07/2023]
Abstract
Under the natural environment, nutrient signals interact with phytohormones to coordinate and reprogram plant growth and survival. Sugars are important molecules that control almost all morphological and physiological processes in plants, ranging from seed germination to senescence. In addition to their functions as energy resources, osmoregulation, storage molecules, and structural components, sugars function as signaling molecules and interact with various plant signaling pathways, such as hormones, stress, and light to modulate growth and development according to fluctuating environmental conditions. Auxin, being an important phytohormone, is associated with almost all stages of the plant's life cycle and also plays a vital role in response to the dynamic environment for better growth and survival. In the previous years, substantial progress has been made that showed a range of common responses mediated by sugars and auxin signaling. This review discusses how sugar signaling affects auxin at various levels from its biosynthesis to perception and downstream gene activation. On the same note, the review also highlights the role of auxin signaling in fine-tuning sugar metabolism and carbon partitioning. Furthermore, we discussed the crosstalk between the two signaling machineries in the regulation of various biological processes, such as gene expression, cell cycle, development, root system architecture, and shoot growth. In conclusion, the review emphasized the role of sugar and auxin crosstalk in the regulation of several agriculturally important traits. Thus, engineering of sugar and auxin signaling pathways could potentially provide new avenues to manipulate for agricultural purposes.
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Affiliation(s)
- Bhuwaneshwar Sharan Mishra
- National Institute of Plant Genome Research, New Delhi, India
- Bhuwaneshwar Sharan Mishra, Ram Gulam Rai P. G. College Banktashiv, Affiliated to Deen Dayal Upadhyaya Gorakhpur University Gorakhpur, Deoria, Uttar Pradesh, India
| | - Mohan Sharma
- National Institute of Plant Genome Research, New Delhi, India
| | - Ashverya Laxmi
- National Institute of Plant Genome Research, New Delhi, India
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30
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Aamir M, Karmakar P, Singh VK, Kashyap SP, Pandey S, Singh BK, Singh PM, Singh J. A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.). PHYSIOLOGIA PLANTARUM 2021; 173:1729-1764. [PMID: 33547804 DOI: 10.1111/ppl.13357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Melon (Cucumis melo L.) is an important cucurbit and has been considered as a model plant for studying sex determination. The four most common sexual morphotypes in melon are monoecious (A-G-M), gynoecious (--ggM-), andromonoecious (A-G-mm), and hermaphrodite (--ggmm). Sex expression in melons is complex, as the genes and associated networks that govern the sex expression are not fully explored. Recently, RNA-seq transcriptomic profiling, ChIP-qPCR analysis integrated with gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathways predicted the differentially expressed genes including sex-specific ACS and ACO genes, in regulating the sex-expression, phytohormonal cross-talk, signal transduction, and secondary metabolism in melons. Integration of transcriptional control through genetic interaction in between the ACS7, ACS11, and WIP1 in epistatic or hypostatic manner, along with the recruitment of H3K9ac and H3K27me3, epigenetically, overall determine sex expression. Alignment of protein sequences for establishing phylogenetic evolution, motif comparison, and protein-protein interaction supported the structural conservation while presence of the conserved hydrophilic and charged residues across the diverged evolutionary group predicted the functional conservation of the ACS protein. Presence of the putative cis-binding elements or DNA motifs, and its further comparison with DAP-seq-based cistrome and epicistrome of Arabidopsis, unraveled strong ancestry of melons with Arabidopsis. Motif comparison analysis also characterized putative genes and transcription factors involved in ethylene biosynthesis, signal transduction, and hormonal cross-talk related to sex expression. Overall, we have comprehensively reviewed research findings for a deeper insight into transcriptional and epigenetic regulation of sex expression and flower development in melons.
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Affiliation(s)
- Mohd Aamir
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Pradip Karmakar
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Vinay Kumar Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Sarvesh Pratap Kashyap
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Sudhakar Pandey
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Binod Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Prabhakar Mohan Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Jagdish Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
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31
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Sow MD, Le Gac AL, Fichot R, Lanciano S, Delaunay A, Le Jan I, Lesage-Descauses MC, Citerne S, Caius J, Brunaud V, Soubigou-Taconnat L, Cochard H, Segura V, Chaparro C, Grunau C, Daviaud C, Tost J, Brignolas F, Strauss SH, Mirouze M, Maury S. RNAi suppression of DNA methylation affects the drought stress response and genome integrity in transgenic poplar. THE NEW PHYTOLOGIST 2021; 232:80-97. [PMID: 34128549 DOI: 10.1111/nph.17555] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/08/2021] [Indexed: 05/27/2023]
Abstract
Trees are long-lived organisms that continuously adapt to their environments, a process in which epigenetic mechanisms are likely to play a key role. Via downregulation of the chromatin remodeler DECREASED IN DNA METHYLATION 1 (DDM1) in poplar (Populus tremula × Populus alba) RNAi lines, we examined how DNA methylation coordinates genomic and physiological responses to moderate water deficit. We compared the growth and drought response of two RNAi-ddm1 lines to wild-type (WT) trees under well-watered and water deficit/rewatering conditions, and analyzed their methylomes, transcriptomes, mobilomes and phytohormone contents in the shoot apical meristem. The RNAi-ddm1 lines were more tolerant to drought-induced cavitation but did not differ in height or stem diameter growth. About 5000 differentially methylated regions were consistently detected in both RNAi-ddm1 lines, colocalizing with 910 genes and 89 active transposable elements. Under water deficit conditions, 136 differentially expressed genes were found, including many involved in phytohormone pathways; changes in phytohormone concentrations were also detected. Finally, the combination of hypomethylation and drought led to the mobility of two transposable elements. Our findings suggest major roles for DNA methylation in regulation of genes involved in hormone-related stress responses, and the maintenance of genome integrity through repression of transposable elements.
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Affiliation(s)
- Mamadou D Sow
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Anne-Laure Le Gac
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Régis Fichot
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Sophie Lanciano
- IRD, UMR 232 DIADE, Université de Montpellier, Montpellier, 34090, France
- Laboratory of Plant Genome and Development, Université de Perpignan, Perpignan, 66860, France
| | - Alain Delaunay
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Isabelle Le Jan
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | | | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Jose Caius
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Hervé Cochard
- Université Clermont Auvergne, INRAE, PIAF, Clermont-Ferrand, 63000, France
| | - Vincent Segura
- BioForA, INRAE, ONF, UMR 0588, Orléans, 45075, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Montpellier SupAgro, UMR 1334, Montpellier, F-34398, France
| | | | - Christoph Grunau
- UMR 5244, IHPE, Université de Perpignan, Perpignan, 66100, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA- Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91057, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA- Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91057, France
| | - Franck Brignolas
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331-5752, USA
| | - Marie Mirouze
- IRD, UMR 232 DIADE, Université de Montpellier, Montpellier, 34090, France
- Laboratory of Plant Genome and Development, Université de Perpignan, Perpignan, 66860, France
| | - Stéphane Maury
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
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Du Q, Qu Z, Wang L, Jiang J, Fu X, Fang Y, Li X, Xie X. Histone deacetylase SbHDT701 in Sorghum bicolor reveals functions in response to stress factors by enhancing acetylation. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 178:104908. [PMID: 34446212 DOI: 10.1016/j.pestbp.2021.104908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Histone acetylation plays important roles in eukaryotic chromatin modification and gene expression regulation. Acetylation levels are modulated by histone deacetylases (HDACs), which function as key epigenetic factors that regulate gene expression in response to various stresses. HDT701, a member of the HD2 subfamily of HDACs, plays crucial roles in plant responses to abiotic stress and pathogen infection. Here, we analysed the expression pattern of SbHDT701 in sorghum. Real-time fluorescence quantitative PCR (RT-qPCR) results showed that expression of SbHDT701 was tissue-specific, and up-regulated under drought (d-mannitol) and salt (NaCl) stresses. We also determined the optimal expression conditions for SbHDT701 protein accumulation, and successfully expressed and purified SbHDT701 protein. Besides, overexpression of SbHDT701 in could promote the growth of recombinant cells under abiotic stress. SbHDT701 expression in Escherichia coli also increased acetylation modification levels following treatment with 750 mM NaCl, and 100 mM or 300 mM d-mannitol. In summary, the sorghum HDAC SbHDT701 mediates stress responses by enhancing acetylation modification levels.
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Affiliation(s)
- Qiaoli Du
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Zhiguang Qu
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Li Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Junmei Jiang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China; State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Xiaodong Fu
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China.
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China.
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Smolikova G, Strygina K, Krylova E, Leonova T, Frolov A, Khlestkina E, Medvedev S. Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects. PLANTS (BASEL, SWITZERLAND) 2021; 10:1884. [PMID: 34579418 PMCID: PMC8467299 DOI: 10.3390/plants10091884] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/02/2021] [Accepted: 09/08/2021] [Indexed: 01/21/2023]
Abstract
Transition from seed to seedling is one of the critical developmental steps, dramatically affecting plant growth and viability. Before plants enter the vegetative phase of their ontogenesis, massive rearrangements of signaling pathways and switching of gene expression programs are required. This results in suppression of the genes controlling seed maturation and activation of those involved in regulation of vegetative growth. At the level of hormonal regulation, these events are controlled by the balance of abscisic acid and gibberellins, although ethylene, auxins, brassinosteroids, cytokinins, and jasmonates are also involved. The key players include the members of the LAFL network-the transcription factors LEAFY COTYLEDON1 and 2 (LEC 1 and 2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (FUS3), as well as DELAY OF GERMINATION1 (DOG1). They are the negative regulators of seed germination and need to be suppressed before seedling development can be initiated. This repressive signal is mediated by chromatin remodeling complexes-POLYCOMB REPRESSIVE COMPLEX 1 and 2 (PRC1 and PRC2), as well as PICKLE (PKL) and PICKLE-RELATED2 (PKR2) proteins. Finally, epigenetic methylation of cytosine residues in DNA, histone post-translational modifications, and post-transcriptional downregulation of seed maturation genes with miRNA are discussed. Here, we summarize recent updates in the study of hormonal and epigenetic switches involved in regulation of the transition from seed germination to the post-germination stage.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ksenia Strygina
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Ekaterina Krylova
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany; (T.L.); (A.F.)
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany; (T.L.); (A.F.)
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena Khlestkina
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia;
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Bennett M, Cleaves K, Hewezi T. Expression Patterns of DNA Methylation and Demethylation Genes during Plant Development and in Response to Phytohormones. Int J Mol Sci 2021; 22:ijms22189681. [PMID: 34575855 PMCID: PMC8470644 DOI: 10.3390/ijms22189681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 01/02/2023] Open
Abstract
DNA methylation and demethylation precisely and effectively modulate gene expression during plant growth and development and in response to stress. However, expression profiles of genes involved in DNA methylation and demethylation during plant development and their responses to phytohormone treatments remain largely unknown. We characterized the spatiotemporal expression patterns of genes involved in de novo methylation, methyl maintenance, and active demethylation in roots, shoots, and reproductive organs using β-glucuronidase (GUS) reporter lines. Promoters of DNA demethylases were generally more highly active at the mature root tissues, whereas the promoters of genes involved in DNA methylation were more highly active at fast-growing root tissues. The promoter activity also implies that methylation status in shoot apex, leaf primordia, floral organs, and developing embryos is under tight equilibrium through the activity of genes involved in DNA methylation and demethylation. The promoter activity of DNA methylation and demethylation-related genes in response to various phytohormone treatments revealed that phytohormones can alter DNA methylation status in specific and redundant ways. Overall, our results illustrate that DNA methylation and demethylation pathways act synergistically and antagonistically in various tissues and in response to phytohormone treatments and point to the existence of hormone-linked methylome regulation mechanisms that may contribute to tissue differentiation and development.
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Li Z, Tang M, Luo D, Kashif MH, Cao S, Zhang W, Hu Y, Huang Z, Yue J, Li R, Chen P. Integrated Methylome and Transcriptome Analyses Reveal the Molecular Mechanism by Which DNA Methylation Regulates Kenaf Flowering. FRONTIERS IN PLANT SCIENCE 2021; 12:709030. [PMID: 34512693 PMCID: PMC8428968 DOI: 10.3389/fpls.2021.709030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/26/2021] [Indexed: 05/03/2023]
Abstract
DNA methylation regulates key biological processes in plants. In this study, kenaf seedlings were pretreated with the DNA methylation inhibitor 5-azacytidine (5-azaC) (at concentrations of 0, 100, 200, 400, and 600 μM), and the results showed that pretreatment with 200 μM 5-azaC promoted flowering most effectively. To elucidate the underlying mechanism, phytohormone, adenosine triphosphate (ATP), and starch contents were determined, and genome-wide DNA methylation and transcriptome analyses were performed on anthers pretreated with 200 μM 5-azaC (5-azaC200) or with no 5-azaC (control conditions; 5-azaC0). Biochemical analysis revealed that 5-azaC pretreatment significantly reduced indoleacetic acid (IAA) and gibberellic acid (GA) contents and significantly increased abscisic acid (ABA) and ATP contents. The starch contents significantly increased in response to 200 and 600 μM 5-azaC. Further genome-wide DNA methylation analysis revealed 451 differentially methylated genes (DMGs) with 209 up- and 242 downregulated genes. Transcriptome analysis showed 3,986 differentially expressed genes (DEGs), with 2,171 up- and 1,815 downregulated genes. Integrated genome-wide DNA methylation and transcriptome analyses revealed 72 genes that were both differentially methylated and differentially expressed. These genes, which included ARFs, PP2C, starch synthase, FLC, PIF1, AGL80, and WRKY32, are involved mainly in plant hormone signal transduction, starch and sucrose metabolism, and flowering regulation and may be involved in early flowering. This study serves as a reference and theoretical basis for kenaf production and provides insights into the effects of DNA methylation on plant growth and development.
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Affiliation(s)
- Zengqiang Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Meiqiong Tang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Dengjie Luo
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Muhammad Haneef Kashif
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Shan Cao
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Wenxian Zhang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Yali Hu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Zhen Huang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Jiao Yue
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Ru Li
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Peng Chen
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
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Wang R, Reng M, Tian S, Liu C, Cheng H, Liu Y, Zhang H, Saqib M, Wei H, Wei Z. Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa. G3 (BETHESDA, MD.) 2021; 11:jkab195. [PMID: 34849817 PMCID: PMC8633455 DOI: 10.1093/g3journal/jkab195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/29/2021] [Indexed: 01/15/2023]
Abstract
We applied miRNA expression profiling method to Populus trichocarpa stems of the three developmental stages, primary stem (PS), transitional stem (TS), and secondary stem (SS), to investigate miRNA species and their regulation on lignocellulosic synthesis and related processes. We obtained 892, 872, and 882 known miRNAs and 1727, 1723, and 1597 novel miRNAs, from PS, TS, and SS, respectively. Comparisons of these miRNA species among different developmental stages led to the identification of 114, 306, and 152 differentially expressed miRNAs (DE-miRNAs), which had 921, 2639, and 2042 candidate target genes (CTGs) in the three respective stages of the same order. Correlation analysis revealed 47, 439, and 71 DE-miRNA-CTG pairs of high negative correlation in PS, TS, and SS, respectively. Through biological process analysis, we finally identified 34, 6, and 76 miRNA-CTG pairs from PS, TS, and SS, respectively, and the miRNA target genes in these pairs regulate or participate lignocellulosic biosynthesis-related biological processes: cell division and differentiation, cell wall modification, secondary cell wall biosynthesis, lignification, and programmed cell death processes. This is the first report on an integrated analysis of genome-wide mRNA and miRNA profilings during multiple phases of poplar stem development. Our analysis results imply that individual miRNAs modulate secondary growth and lignocellulosic biosynthesis through regulating transcription factors and lignocellulosic biosynthetic pathway genes, resulting in more dynamic promotion, suppression, or regulatory circuits. This study advanced our understanding of many individual miRNAs and their essential, diversified roles in the dynamic regulation of secondary growth in woody tree species.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Mengxuan Reng
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China
| | - Shuanghui Tian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Cong Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - He Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Huaxin Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China
| | - Muhammad Saqib
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Hairong Wei
- College of Forest Resource and Environmental Science, Michigan Technological University, Houghton MI49931, USA
| | - Zhigang Wei
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China
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Vall-Llaura N, Torres R, Lindo-García V, Muñoz P, Munné-Bosch S, Larrigaudière C, Teixidó N, Giné-Bordonaba J. PbSRT1 and PbSRT2 regulate pear growth and ripening yet displaying a species-specific regulation in comparison to other Rosaceae spp. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 308:110925. [PMID: 34034873 DOI: 10.1016/j.plantsci.2021.110925] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/15/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
Epigenetic regulation is crucial to ensure a coordinated control of the different events that occur during fruit development and ripening. Sirtuins are NAD+-dependent histone deacetylases involved in the regulation of gene expression of many biological processes. However, their implications in the Rosaceae family remains unexplored. Accordingly, in this work, we demonstrated the phylogenetic divergence of both sirtuins among Rosaceae species. We then characterized the expression pattern of both SRT1 and SRT2 in selected pome and stone fruit species. Both SRT1 and SRT2 significantly changed during the fruit development and ripening of apple, nectarine and pear fruit, displaying a different expression profile. Such differences could explain in part their different ripening behaviour. To further unravel the role of sirtuins on the fruit development and ripening processes, a deeper analysis was performed using pear as a fruit model. In pear, PbSRT1 gene expression levels were negatively correlated with specific hormones (i.e. abscisic acid, indole-3-acetic acid, gibberellin A1 and zeatin) during the first phases of fruit development. PbSRT2 seemed to directly mediate pear ripening in an ethylene-independent manner. This hypothesis was further reinforced by treating the fruit with the ethylene inhibitor 1-methylcyclopropene (1-MCP). Instead, enhanced PbSRT2 along pear growth/ripening positively correlated with the accumulation of major sugars (R2 > 0.94), reinforcing the idea that sugar metabolism may be a target of epigenetic modifications during fruit ripening. Overall, the results from this study point out, for the first time, the importance that sirtuins have in the regulation of fruit growth and ripening of pear fruit by likely regulating hormonal and sugar metabolism.
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Affiliation(s)
- Núria Vall-Llaura
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
| | - Rosario Torres
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
| | - Violeta Lindo-García
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
| | - Paula Muñoz
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, 08028, Spain; Institut de Nutrició i Seguretat Alimentària (INSA), University of Barcelona, Barcelona, 08028, Spain.
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, 08028, Spain; Institut de Nutrició i Seguretat Alimentària (INSA), University of Barcelona, Barcelona, 08028, Spain.
| | - Christian Larrigaudière
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
| | - Neus Teixidó
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
| | - Jordi Giné-Bordonaba
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
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38
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Reinvigoration/Rejuvenation Induced through Micrografting of Tree Species: Signaling through Graft Union. PLANTS 2021; 10:plants10061197. [PMID: 34208406 PMCID: PMC8231136 DOI: 10.3390/plants10061197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 02/05/2023]
Abstract
Trees have a distinctive and generally long juvenile period during which vegetative growth rate is rapid and floral organs do not differentiate. Among trees, the juvenile period can range from 1 year to 15–20 years, although with some forest tree species, it can be longer. Vegetative propagation of trees is usually much easier during the juvenile phase than with mature phase materials. Therefore, reversal of maturity is often necessary in order to obtain materials in which rooting ability has been restored. Micrografting has been developed for trees to address reinvigoration/rejuvenation of elite selections to facilitate vegetative propagation. Generally, shoots obtained after serial grafting have increased rooting competence and develop juvenile traits; in some cases, graft-derived shoots show enhanced in vitro proliferation. Recent advances in graft signaling have shown that several factors, e.g., plant hormones, proteins, and different types of RNA, could be responsible for changes in the scion. The focus of this review includes (1) a discussion of the differences between the juvenile and mature growth phases in trees, (2) successful restoration of juvenile traits through micrografting, and (3) the nature of the different signals passing through the graft union.
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Chen Q, Liu K, Yu R, Zhou B, Huang P, Cao Z, Zhou Y, Wang J. From "Dark Matter" to "Star": Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs. FRONTIERS IN PLANT SCIENCE 2021; 12:650926. [PMID: 34163498 PMCID: PMC8215657 DOI: 10.3389/fpls.2021.650926] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/05/2021] [Indexed: 05/27/2023]
Abstract
Long non-coding RNAs (lncRNAs) play a vital role in a variety of biological functions in plant growth and development. In this study, we provided an overview of the molecular mechanisms of lncRNAs in interacting with other biomolecules with an emphasis on those lncRNAs validated only by low-throughput experiments. LncRNAs function through playing multiple roles, including sponger for sequestering RNA or DNA, guider or decoy for recruiting or hijacking transcription factors or peptides, and scaffold for binding with chromatin modification complexes, as well as precursor of microRNAs or small interfering RNAs. These regulatory roles have been validated in several plant species with a comprehensive list of 73 lncRNA-molecule interaction pairs in 16 plant species found so far, suggesting their commonality in the plant kingdom. Such initial findings of a small number of functional plant lncRNAs represent the beginning of what is to come as lncRNAs with unknown functions were found in orders of magnitude more than proteins.
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Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Kui Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Ru Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Bailing Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Pingping Huang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- Peking University Shenzhen Graduate School, Shenzhen, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
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Samo N, Ebert A, Kopka J, Mozgová I. Plant chromatin, metabolism and development - an intricate crosstalk. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102002. [PMID: 33497897 DOI: 10.1016/j.pbi.2021.102002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Chromatin structure influences DNA accessibility and underlying gene expression. Disturbances of chromatin structure often result in pleiotropic developmental phenotypes. Interactions between chromatin modifications and development have been the main focus of epigenetic studies. Recent years brought major advance in uncovering and understanding connections between chromatin organisation in the nucleus and metabolic processes that take place in the cytoplasm or other cellular compartments. Products of primary metabolism and cell redox states influence chromatin-modifying complexes, and chromatin modifiers in turn affect expression of metabolic genes. Current evidence indicates that complex interaction loops between these biological system layers exist. Applying interdisciplinary and holistic approaches will decipher causality and molecular mechanisms of the dynamic crosstalk between chromatin structure, metabolism and plant growth and development.
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Affiliation(s)
- Naseem Samo
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Alina Ebert
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Iva Mozgová
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic.
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41
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Elevated Temperature Induced Adaptive Responses of Two Lupine Species at Early Seedling Phase. PLANTS 2021; 10:plants10061091. [PMID: 34072415 PMCID: PMC8228099 DOI: 10.3390/plants10061091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/26/2022]
Abstract
This study aimed to investigate the impact of climate warming on hormonal traits of invasive and non-invasive plants at the early developmental stage. Two different lupine species—invasive Lupinus polyphyllus Lindl. and non-invasive Lupinus luteus L.—were used in this study. Plants were grown in climate chambers under optimal (25 °C) and simulated climate warming conditions (30 °C). The content of phytohormone indole-3-acetic acid (IAA), ethylene production and the adaptive growth of both species were studied in four-day-old seedlings. A higher content of total IAA, especially of IAA-amides and transportable IAA, as well as higher ethylene emission, was determined to be characteristic for invasive lupine both under optimal and simulated warming conditions. It should be noted that IAA-L-alanine was detected entirely in the invasive plants under both growth temperatures. Further, the ethylene emission values increased significantly in invasive lupine hypocotyls under 30 °C. Invasive plants showed plasticity in their response by reducing growth in a timely manner and adapting to the rise in temperature. Based on the data of the current study, it can be suggested that the invasiveness of both species may be altered under climate warming conditions.
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Xu X, Smaczniak C, Muino JM, Kaufmann K. Cell identity specification in plants: lessons from flower development. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4202-4217. [PMID: 33865238 PMCID: PMC8163053 DOI: 10.1093/jxb/erab110] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/12/2021] [Indexed: 05/15/2023]
Abstract
Multicellular organisms display a fascinating complexity of cellular identities and patterns of diversification. The concept of 'cell type' aims to describe and categorize this complexity. In this review, we discuss the traditional concept of cell types and highlight the impact of single-cell technologies and spatial omics on the understanding of cellular differentiation in plants. We summarize and compare position-based and lineage-based mechanisms of cell identity specification using flower development as a model system. More than understanding ontogenetic origins of differentiated cells, an important question in plant science is to understand their position- and developmental stage-specific heterogeneity. Combinatorial action and crosstalk of external and internal signals is the key to cellular heterogeneity, often converging on transcription factors that orchestrate gene expression programs.
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Affiliation(s)
- Xiaocai Xu
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cezary Smaczniak
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jose M Muino
- Systems Biology of Gene Regulation, Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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In Arabidopsis thaliana Cd differentially impacts on hormone genetic pathways in the methylation defective ddc mutant compared to wild type. Sci Rep 2021; 11:10965. [PMID: 34040101 PMCID: PMC8154917 DOI: 10.1038/s41598-021-90528-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/12/2021] [Indexed: 12/14/2022] Open
Abstract
DNA methylation plays an important role in modulating plant growth plasticity in response to stress, but mechanisms involved in such control need further investigation. We used drm1 drm2 cmt3 mutant of Arabidopsis thaliana, defective in DNA methylation, to explore metabolic pathways downstream epigenetic modulation under cadmium (Cd) stress. To this aim, a transcriptomic analysis was performed on ddc and WT plants exposed to a long-lasting (21 d) Cd treatment (25/50 µM), focusing on hormone genetic pathways. Growth parameters and hormones amount were also estimated. Transcriptomic data and hormone quantification showed that, under prolonged Cd treatment, level and signalling of growth-sustaining hormones (auxins, CKs, GAs) were enhanced and/or maintained, while a decrease was detected for stress-related hormones (JA, ABA, SA), likely as a strategy to avoid the side effects of their long-lasting activation. Such picture was more effective in ddc than WT, already at 25 µM Cd, in line with its better growth performance. A tight relationship between methylation status and the modulation of hormone genetic pathways under Cd stress was assessed. We propose that the higher genome plasticity conferred to ddc by DNA hypomethylated status underlies its prompt response to modulate hormones genetic pathways and activity and assure a flexible growth.
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Nitrogen Starvation-Responsive MicroRNAs Are Affected by Transgenerational Stress in Durum Wheat Seedlings. PLANTS 2021; 10:plants10050826. [PMID: 33919185 PMCID: PMC8143135 DOI: 10.3390/plants10050826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022]
Abstract
Stress events have transgenerational effects on plant growth and development. In Mediterranean regions, water-deficit and heat (WH) stress is a frequent issue that negatively affects crop yield and quality. Nitrogen (N) is an essential plant macronutrient and often a yield-limiting factor for crops. Here, the response of durum wheat seedlings to N starvation under the transgenerational effects of WH stress was investigated in two genotypes. Both genotypes showed a significant reduction in seedling height, leaf number, shoot and root weight (fresh and dry), primary root length, and chlorophyll content under N starvation stress. However, in the WH stress-tolerant genotype, the percentage reduction of most traits was lower in progeny from the stressed parents than progeny from the control parents. Small RNA sequencing identified 1534 microRNAs in different treatment groups. Differentially expressed microRNAs (DEMs) were characterized subject to N starvation, parental stress and genotype factors, with their target genes identified in silico. GO and KEGG enrichment analyses revealed the biological functions, associated with DEM-target modules in stress adaptation processes, that could contribute to the phenotypic differences observed between the two genotypes. The study provides the first evidence of the transgenerational effects of WH stress on the N starvation response in durum wheat.
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Liu H, Timko MP. Jasmonic Acid Signaling and Molecular Crosstalk with Other Phytohormones. Int J Mol Sci 2021; 22:ijms22062914. [PMID: 33805647 PMCID: PMC8000993 DOI: 10.3390/ijms22062914] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022] Open
Abstract
Plants continually monitor their innate developmental status and external environment and make adjustments to balance growth, differentiation and stress responses using a complex and highly interconnected regulatory network composed of various signaling molecules and regulatory proteins. Phytohormones are an essential group of signaling molecules that work through a variety of different pathways conferring plasticity to adapt to the everchanging developmental and environmental cues. Of these, jasmonic acid (JA), a lipid-derived molecule, plays an essential function in controlling many different plant developmental and stress responses. In the past decades, significant progress has been made in our understanding of the molecular mechanisms that underlie JA metabolism, perception, signal transduction and its crosstalk with other phytohormone signaling pathways. In this review, we discuss the JA signaling pathways starting from its biosynthesis to JA-responsive gene expression, highlighting recent advances made in defining the key transcription factors and transcriptional regulatory proteins involved. We also discuss the nature and degree of crosstalk between JA and other phytohormone signaling pathways, highlighting recent breakthroughs that broaden our knowledge of the molecular bases underlying JA-regulated processes during plant development and biotic stress responses.
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Vigneaud J, Maury S. [Developmental plasticity in plants: an interaction between hormones and epigenetics at the meristem level]. Biol Aujourdhui 2020; 214:125-135. [PMID: 33357371 DOI: 10.1051/jbio/2020011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 12/25/2022]
Abstract
Plants are fixed organisms with continuous development throughout their life and great sensitivity to environmental variations. They react in this way by exhibiting large developmental phenotypic plasticity. This plasticity is partly controlled by (phyto)hormones, but recent studies also suggest the involvement of epigenetic mechanisms. It seems that these two factors may interact in a complex way and especially in the stem cells grouped together in meristems. The objective of this review is to present the current arguments about this interaction which would promote developmental plasticity. Three major points are thus addressed to justify this interaction between hormonal control and epigenetics (control at the chromatin level) for the developmental plasticity of plants: the arguments in favor of an effect of hormones on chromatin and vice versa, the arguments in favor of their roles on developmental plasticity and finally the arguments in favor of the central place of these interactions, the meristems. Various perspectives and applications are discussed.
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Affiliation(s)
- Julien Vigneaud
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAe, Université d'Orléans, EA1207 USC1328, 45067 Orléans, France
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAe, Université d'Orléans, EA1207 USC1328, 45067 Orléans, France
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Yoshida H, Nakajima M, Matsuoka M. Special Issue on Gibberellin: A Fascinating Substance That Still Attracts Plant Scientists. PLANT & CELL PHYSIOLOGY 2020; 61:1829-1831. [PMID: 33057646 DOI: 10.1093/pcp/pcaa127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Hideki Yoshida
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Nagoya, 464-8601 Japan
| | - Masatoshi Nakajima
- Department of Applied Biological Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Nagoya, 464-8601 Japan
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Jung C, Nguyen NH, Cheong JJ. Transcriptional Regulation of Protein Phosphatase 2C Genes to Modulate Abscisic Acid Signaling. Int J Mol Sci 2020; 21:ijms21249517. [PMID: 33327661 PMCID: PMC7765119 DOI: 10.3390/ijms21249517] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/04/2020] [Accepted: 12/12/2020] [Indexed: 01/04/2023] Open
Abstract
The plant hormone abscisic acid (ABA) triggers cellular tolerance responses to osmotic stress caused by drought and salinity. ABA controls the turgor pressure of guard cells in the plant epidermis, leading to stomatal closure to minimize water loss. However, stomatal apertures open to uptake CO2 for photosynthesis even under stress conditions. ABA modulates its signaling pathway via negative feedback regulation to maintain plant homeostasis. In the nuclei of guard cells, the clade A type 2C protein phosphatases (PP2Cs) counteract SnRK2 kinases by physical interaction, and thereby inhibit activation of the transcription factors that mediate ABA-responsive gene expression. Under osmotic stress conditions, PP2Cs bind to soluble ABA receptors to capture ABA and release active SnRK2s. Thus, PP2Cs function as a switch at the center of the ABA signaling network. ABA induces the expression of genes encoding repressors or activators of PP2C gene transcription. These regulators mediate the conversion of PP2C chromatins from a repressive to an active state for gene transcription. The stress-induced chromatin remodeling states of ABA-responsive genes could be memorized and transmitted to plant progeny; i.e., transgenerational epigenetic inheritance. This review focuses on the mechanism by which PP2C gene transcription modulates ABA signaling.
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Affiliation(s)
- Choonkyun Jung
- Department of International Agricultural Technology and Crop Biotechnology, Institute/Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea;
- Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Nguyen Hoai Nguyen
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City 700000, Vietnam;
| | - Jong-Joo Cheong
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
- Correspondence: ; Tel.: +82-2-880-4888; Fax: +82-2-873-5260
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Borges F, Donoghue MTA, LeBlanc C, Wear EE, Tanurdžić M, Berube B, Brooks A, Thompson WF, Hanley-Bowdoin L, Martienssen RA. Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation. Curr Biol 2020; 31:591-600.e4. [PMID: 33275892 DOI: 10.1016/j.cub.2020.10.098] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/24/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, whereas mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, whereas mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small interfering RNAs (siRNAs) and histone H3 lysine dimethylation (H3K9me2), without gaining CHH methylation. This suggests that spontaneous epialleles that arise in plant cell cultures are stably maintained by siRNA and H3K9me2 independent of the canonical RNA-directed DNA methylation (RdDM) pathway. In contrast, loci that fail to produce siRNA may be targeted for demethylation when the cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small-RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.
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Affiliation(s)
- Filipe Borges
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Mark T A Donoghue
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Emily E Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Milos Tanurdžić
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Benjamin Berube
- Cold Spring Harbor Laboratory School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ashley Brooks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - William F Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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Genitoni J, Vassaux D, Delaunay A, Citerne S, Portillo Lemus L, Etienne MP, Renault D, Stoeckel S, Barloy D, Maury S. Hypomethylation of the aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala mimics the adaptive transition into the terrestrial morphotype. PHYSIOLOGIA PLANTARUM 2020; 170:280-298. [PMID: 32623739 DOI: 10.1111/ppl.13162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 06/17/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Ongoing global changes affect ecosystems and open up new opportunities for biological invasion. The ability of invasive species to rapidly adapt to new environments represents a relevant model for studying short-term adaptation mechanisms. The aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala, is classified as harmful in European rivers. In French wet meadows, this species has shown a rapid transition from aquatic to terrestrial environments with emergence of two distinct morphotypes in 5 years. To understand the heritable mechanisms involved in adjustment to such a new environment, we investigate both genetic and epigenetic as possible sources of flexibility involved in this fast terrestrial transition. We found a low overall genetic differentiation between the two morphotypes arguing against the possibility that terrestrial morphotype emerged from a new adaptive genetic capacity. Artificial hypomethylation was induced on both morphotypes to assess the epigenetic hypothesis. We analyzed global DNA methylation, morphological changes, phytohormones and metabolite profiles of both morphotype responses in both aquatic and terrestrial conditions in shoot and root tissues. Hypomethylation significantly affected morphological variables, phytohormone levels and the amount of some metabolites. The effects of hypomethylation depended on morphotypes, conditions and plant tissues, which highlighted differences among the morphotypes and their plasticity. Using a correlative integrative approach, we showed that hypomethylation of the aquatic morphotype mimicked the characteristics of the terrestrial morphotype. Our data suggest that DNA methylation rather than a new adaptive genetic capacity is playing a key role in L. grandiflora subsp. hexapetala plasticity during its rapid aquatic to terrestrial transition.
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Affiliation(s)
- Julien Genitoni
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
| | - Danièle Vassaux
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Alain Delaunay
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Luis Portillo Lemus
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Marie-Pierre Etienne
- Institut Agro, CNRS, Université Rennes, IRMAR (Institut de Recherche Mathématique de Rennes) - UMR 6625, Rennes, F-35000, France
| | - David Renault
- UMR CNRS 6553 EcoBio, University of Rennes 1, Rennes, France
- Institut Universitaire de France, 1 rue Descartes, Paris, France
| | - Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université Rennes, Le Rheu, 35653, France
| | - Dominique Barloy
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
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