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Carrera-Castaño G, Calleja-Cabrera J, Pernas M, Gómez L, Oñate-Sánchez L. An Updated Overview on the Regulation of Seed Germination. PLANTS 2020; 9:plants9060703. [PMID: 32492790 PMCID: PMC7356954 DOI: 10.3390/plants9060703] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023]
Abstract
The ability of a seed to germinate and establish a plant at the right time of year is of vital importance from an ecological and economical point of view. Due to the fragility of these early growth stages, their swiftness and robustness will impact later developmental stages and crop yield. These traits are modulated by a continuous interaction between the genetic makeup of the plant and the environment from seed production to germination stages. In this review, we have summarized the established knowledge on the control of seed germination from a molecular and a genetic perspective. This serves as a “backbone” to integrate the latest developments in the field. These include the link of germination to events occurring in the mother plant influenced by the environment, the impact of changes in the chromatin landscape, the discovery of new players and new insights related to well-known master regulators. Finally, results from recent studies on hormone transport, signaling, and biophysical and mechanical tissue properties are underscoring the relevance of tissue-specific regulation and the interplay of signals in this crucial developmental process.
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52
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Matilla AJ. Auxin: Hormonal Signal Required for Seed Development and Dormancy. PLANTS (BASEL, SWITZERLAND) 2020; 9:E705. [PMID: 32492815 PMCID: PMC7356396 DOI: 10.3390/plants9060705] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022]
Abstract
The production of viable seeds is a key event in the life cycle of higher plants. Historically, abscisic acid (ABA) and gibberellin (GAs) were considered the main hormones that regulate seed formation. However, auxin has recently emerged as an essential player that modulates, in conjunction with ABA, different cellular processes involved in seed development as well as the induction, regulation and maintenance of primary dormancy (PD). This review examines and discusses the key role of auxin as a signaling molecule that coordinates seed life. The cellular machinery involved in the synthesis and transport of auxin, as well as their cellular and tissue compartmentalization, is crucial for the development of the endosperm and seed-coat. Thus, auxin is an essential compound involved in integuments development, and its transport from endosperm is regulated by AGAMOUS-LIKE62 (AGL62) whose transcript is specifically expressed in the endosperm. In addition, recent biochemical and genetic evidence supports the involvement of auxins in PD. In this process, the participation of the transcriptional regulator ABA INSENSITIVE3 (ABI3) is critical, revealing a cross-talk between auxin and ABA signaling. Future experimental aimed at advancing knowledge of the role of auxins in seed development and PD are also discussed.
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Affiliation(s)
- Angel J Matilla
- Departamento de Biología Funcional (Área Fisiología Vegetal), Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Choi MG, Kim EJ, Song JY, Choi SB, Cho SW, Park CS, Kang CS, Park YI. Peptide transporter2 (PTR2) enhances water uptake during early seed germination in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2020; 102:615-624. [PMID: 31997111 PMCID: PMC7062858 DOI: 10.1007/s11103-020-00967-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/10/2020] [Indexed: 05/12/2023]
Abstract
PTR2 in Arabidopsis thaliana is negatively regulated by ABI4 and plays a key role in water uptake by seeds, ensuring that imbibed seeds proceed to germination. Peptide transporters (PTRs) transport nitrogen-containing substrates in a proton-dependent manner. Among the six PTRs in Arabidopsis thaliana, the physiological role of the tonoplast-localized, seed embryo abundant PTR2 is unknown. In the present study, a molecular physiological analysis of PTR2 was conducted using ptr2 mutants and PTR2CO complementation lines. Compared with the wild type, the ptr2 mutant showed ca. 6 h delay in testa rupture and consequently endosperm rupture because of 17% lower water content and 10% higher free abscisic acid (ABA) content. Constitutive overexpression of the PTR2 gene under the control of the Cauliflower mosaic virus (CaMV) 35S promoter in ptr2 mutants rescued the mutant phenotypes. After cold stratification, a transient increase in ABA INSENSITIVE4 (ABI4) transcript levels during induction of testa rupture was followed by a similar increase in PTR2 transcript levels, which peaked prior to endosperm rupture. The PTR2 promoter region containing multiple CCAC motifs was recognized by ABI4 in electrophoretic mobility shift assays, and PTR2 expression was repressed by 67% in ABI4 overexpression lines compared with the wild type, suggesting that PTR2 is an immediate downstream target of ABI4. Taken together, the results suggest that ABI4-dependent temporal regulation of PTR2 expression may influence water status during seed germination to promote the post-germinative growth of imbibed seeds.
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Affiliation(s)
- Myoung-Goo Choi
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
- National Institute of Crop Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Eui Joong Kim
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ji-Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Gyunggi-do, Republic of Korea
| | - Seong-Woo Cho
- Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju, 54896, Republic of Korea
| | - Chul Soo Park
- Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju, 54896, Republic of Korea
| | - Chon-Sik Kang
- National Institute of Crop Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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54
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Buijs G, Vogelzang A, Nijveen H, Bentsink L. Dormancy cycling: translation-related transcripts are the main difference between dormant and non-dormant seeds in the field. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:327-339. [PMID: 31785171 PMCID: PMC7217185 DOI: 10.1111/tpj.14626] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 05/20/2023]
Abstract
Primary seed dormancy is a mechanism that orchestrates the timing of seed germination in order to prevent out-of-season germination. Secondary dormancy can be induced in imbibed seeds when they encounter prolonged unfavourable conditions. Secondary dormancy is not induced during dry storage, and therefore the mechanisms underlying this process have remained largely unexplored. Here, a 2-year seed burial experiment in which dormancy cycling was studied at the physiological and transcriptional level is presented. For these analyses six different Arabidopsis thaliana genotypes were used: Landsberg erecta (Ler) and the dormancy associated DELAY OF GERMINATION (DOG) near-isogenic lines 1, 2, 3, 6 and 22 (NILDOG1, 2, 3, 6 and 22). The germination potential of seeds exhumed from the field showed that these seeds go through dormancy cycling and that the dynamics of this cycling is genotype dependent. RNA-seq analysis revealed large transcriptional changes during dormancy cycling, especially at the time points preceding shifts in dormancy status. Dormancy cycling is driven by soil temperature and the endosperm is important in the perception of the environment. Genes that are upregulated in the low- to non-dormant stages are enriched for genes involved in translation, indicating that the non-dormant seeds are prepared for rapid seed germination.
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Affiliation(s)
- Gonda Buijs
- Wageningen Seed LaboratoryLaboratory of Plant PhysiologyWageningen UniversityWageningenthe Netherlands
| | - Afke Vogelzang
- Wageningen Seed LaboratoryLaboratory of Plant PhysiologyWageningen UniversityWageningenthe Netherlands
| | - Harm Nijveen
- Bioinformatics GroupWageningen UniversityWageningenthe Netherlands
| | - Leónie Bentsink
- Wageningen Seed LaboratoryLaboratory of Plant PhysiologyWageningen UniversityWageningenthe Netherlands
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55
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Hoai PTT, Tyerman SD, Schnell N, Tucker M, McGaughey SA, Qiu J, Groszmann M, Byrt CS. Deciphering aquaporin regulation and roles in seed biology. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1763-1773. [PMID: 32109278 DOI: 10.1093/jxb/erz555] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/26/2020] [Indexed: 05/25/2023]
Abstract
Seeds are the typical dispersal and propagation units of angiosperms and gymnosperms. Water movement into and out of seeds plays a crucial role from the point of fertilization through to imbibition and seed germination. A class of membrane intrinsic proteins called aquaporins (AQPs) assist with the movement of water and other solutes within seeds. These highly diverse and abundant proteins are associated with different processes in the development, longevity, imbibition, and germination of seed. However, there are many AQPs encoded in a plant's genome and it is not yet clear how, when, or which AQPs are involved in critical stages of seed biology. Here we review the literature to examine the evidence for AQP involvement in seeds and analyse Arabidopsis seed-related transcriptomic data to assess which AQPs are likely to be important in seed water relations and explore additional roles for AQPs in seed biology.
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Affiliation(s)
- Phan T T Hoai
- Australian Research Council Centre of Excellence in Plant Energy Biology, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- Faculty of Agriculture and Forestry, Tay Nguyen University, Dak Lak, Viet Nam
| | - Stephen D Tyerman
- Australian Research Council Centre of Excellence in Plant Energy Biology, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
| | - Nicholas Schnell
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
| | - Matthew Tucker
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
| | - Samantha A McGaughey
- Australian Research Council Centre of Excellence in Plant Energy Biology, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
| | - Jiaen Qiu
- Australian Research Council Centre of Excellence in Plant Energy Biology, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
| | - Michael Groszmann
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Caitlin S Byrt
- Australian Research Council Centre of Excellence in Plant Energy Biology, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, Australia
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56
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Footitt S, Walley PG, Lynn JR, Hambidge AJ, Penfield S, Finch‐Savage WE. Trait analysis reveals DOG1 determines initial depth of seed dormancy, but not changes during dormancy cycling that result in seedling emergence timing. THE NEW PHYTOLOGIST 2020; 225:2035-2047. [PMID: 31359436 PMCID: PMC7027856 DOI: 10.1111/nph.16081] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/20/2019] [Indexed: 05/22/2023]
Abstract
Seedling emergence timing is crucial in competitive plant communities and so contributes to species fitness. To understand the mechanistic basis of variation in seedling emergence timing, we exploited the contrasting behaviour of two Arabidopsis thaliana ecotypes: Cape Verde Islands (Cvi) and Burren (Bur-0). We used RNA-Seq analysis of RNA from exhumed seeds and quantitative trait loci (QTL) analyses on a mapping population from crossing the Cvi and Bur-0 ecotypes. We determined genome-wide expression patterns over an annual dormancy cycle in both ecotypes, identifying nine major clusters based on the seasonal timing of gene expression, and variation in behaviour between them. QTL were identified for depth of seed dormancy and seedling emergence timing (SET). Both analyses showed a key role for DOG1 in determining depth of dormancy, but did not support a direct role for DOG1 in generating altered seasonal patterns of seedling emergence. The principle QTL determining SET (SET1: dormancy cycling) is physically close on chromosome 5, but is distinct from DOG1. We show that SET1 and two other SET QTLs each contain a candidate gene (AHG1, ANAC060, PDF1 respectively) closely associated with DOG1 and abscisic acid signalling and suggest a model for the control of SET in the field.
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Affiliation(s)
- Steven Footitt
- School of Life SciencesUniversity of WarwickWellesbourne CampusWarwickshireCV35 9EFUK
| | - Peter G. Walley
- Functional and Comparative GenomicsInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUK
| | - James R. Lynn
- Applied Statistical SolutionsBishops TachbrookLeamingtonCV33 9RJUK
| | - Angela J. Hambidge
- School of Life SciencesUniversity of WarwickWellesbourne CampusWarwickshireCV35 9EFUK
| | - Steven Penfield
- Department of Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
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57
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Affiliation(s)
- Steven M Smith
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7001, Australia
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7001, Australia
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58
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Liew LC, Narsai R, Wang Y, Berkowitz O, Whelan J, Lewsey MG. Temporal tissue-specific regulation of transcriptomes during barley (Hordeum vulgare) seed germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:700-715. [PMID: 31628689 DOI: 10.1111/tpj.14574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/09/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
The distinct functions of individual cell types require cells to express specific sets of genes. The germinating seed is an excellent model to study genome regulation between cell types since the majority of the transcriptome is differentially expressed in a short period, beginning from a uniform, metabolically inactive state. In this study, we applied laser-capture microdissection RNA-sequencing to small numbers of cells from the plumule, radicle tip and scutellum of germinating barley seeds every 8 h, over a 48 h time course. Tissue-specific gene expression was notably common; 25% (910) of differentially expressed transcripts in plumule, 34% (1876) in radicle tip and 41% (2562) in scutellum were exclusive to that organ. We also determined that tissue-specific storage of transcripts occurs during seed development and maturation. Co-expression of genes had strong spatiotemporal structure, with most co-expression occurring within one organ and at a subset of specific time points during germination. Overlapping and distinct enrichment of functional categories were observed in the tissue-specific profiles. We identified candidate transcription factors amongst these that may be regulators of spatiotemporal gene expression programs. Our findings contribute to the broader goal of generating an integrative model that describes the structure and function of individual cells within seeds during germination.
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Affiliation(s)
- Lim Chee Liew
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Reena Narsai
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Yan Wang
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
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59
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Cao H, Han Y, Li J, Ding M, Li Y, Li X, Chen F, Soppe WJ, Liu Y. Arabidopsis thaliana SEED DORMANCY 4-LIKE regulates dormancy and germination by mediating the gibberellin pathway. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:919-933. [PMID: 31641755 DOI: 10.1093/jxb/erz471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
The molecular mechanisms underlying seed dormancy and germination are not fully understood. Here, we show that Arabidopsis thaliana SEED DORMANCY 4-LIKE (AtSdr4L) is a novel specific regulator of dormancy and germination. AtSdr4L encodes a protein with an unknown biochemical function that is localized in the nucleus and is expressed specifically in seeds. Loss of function of AtSdr4L results in increased seed dormancy. The germination of freshly harvested seeds of the Atsdr4l mutant is insensitive to gibberellin (GA). After-ripened mutant seeds are hypersensitive to the GA biosynthesis-inhibitor paclobutrazol but show unaltered sensitivity to abscisic acid. Several GA biosynthesis genes and GA-regulated cell wall remodeling genes are down-regulated in the mutant in both dormant and after-ripened seeds. These results suggest that the Atsdr4l mutation causes both decreased GA biosynthesis and reduced responses. In addition, a genetic analysis indicated that AtSdr4L is epistatic to DELAY OF GERMINATION1 (DOG1) for dormancy and acts upstream of RGA-LIKE 2 (RGL2) in the GA pathway. We propose that AtSdr4L regulates seed dormancy and germination by mediating both the DOG1 and GA pathways.
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Affiliation(s)
- Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yi Han
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Shandong Provincial Center of Forest Tree Germplasm Resources, Jinan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingyi Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meng Ding
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoying Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wim Jj Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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60
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Xu P, Tang G, Cui W, Chen G, Ma CL, Zhu J, Li P, Shan L, Liu Z, Wan S. Transcriptional Differences in Peanut (Arachis hypogaea L.) Seeds at the Freshly Harvested, After-ripening and Newly Germinated Seed Stages: Insights into the Regulatory Networks of Seed Dormancy Release and Germination. PLoS One 2020; 15:e0219413. [PMID: 31899920 PMCID: PMC6941926 DOI: 10.1371/journal.pone.0219413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/05/2019] [Indexed: 12/27/2022] Open
Abstract
Seed dormancy and germination are the two important traits related to plant survival, reproduction and crop yield. To understand the regulatory mechanisms of these traits, it is crucial to clarify which genes or pathways participate in the regulation of these processes. However, little information is available on seed dormancy and germination in peanut. In this study, seeds of the variety Luhua No.14, which undergoes nondeep dormancy, were selected, and their transcriptional changes at three different developmental stages, the freshly harvested seed (FS), the after-ripening seed (DS) and the newly germinated seed (GS) stages, were investigated by comparative transcriptomic analysis. The results showed that genes with increased transcription in the DS vs FS comparison were overrepresented for oxidative phosphorylation, the glycolysis pathway and the tricarboxylic acid (TCA) cycle, suggesting that after a period of dry storage, the intermediates stored in the dry seeds were rapidly mobilized by glycolysis, the TCA cycle, the glyoxylate cycle, etc.; the electron transport chain accompanied by respiration was reactivated to provide ATP for the mobilization of other reserves and for seed germination. In the GS vs DS pairwise comparison, dozens of the upregulated genes were related to plant hormone biosynthesis and signal transduction, including the majority of components involved in the auxin signal pathway, brassinosteroid biosynthesis and signal transduction as well as some GA and ABA signal transduction genes. During seed germination, the expression of some EXPANSIN and XYLOGLUCAN ENDOTRANSGLYCOSYLASE genes was also significantly enhanced. To investigate the effects of different hormones during seed germination, the contents and differential distribution of ABA, GAs, BRs and IAA in the cotyledons, hypocotyls and radicles, and plumules of three seed sections at different developmental stages were also investigated. Combined with previous data in other species, it was suggested that the coordination of multiple hormone signal transduction nets plays a key role in radicle protrusion and seed germination.
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Affiliation(s)
- Pingli Xu
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong, China
| | - Guiying Tang
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong, China
| | - Weipei Cui
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong, China
- College of Life Science, Shandong Normal University, Jinan, Shandong, China
| | | | - Chang-Le Ma
- College of Life Science, Shandong Normal University, Jinan, Shandong, China
| | - Jieqiong Zhu
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong, China
- College of Life Science, Shandong Normal University, Jinan, Shandong, China
| | - Pengxiang Li
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong, China
- College of Life Science, Shandong Normal University, Jinan, Shandong, China
| | - Lei Shan
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong, China
- College of Life Science, Shandong Normal University, Jinan, Shandong, China
- * E-mail: (LS); (ZL); (SW)
| | - Zhanji Liu
- Shandong Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- * E-mail: (LS); (ZL); (SW)
| | - Shubo Wan
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong, China
- College of Life Science, Shandong Normal University, Jinan, Shandong, China
- * E-mail: (LS); (ZL); (SW)
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61
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Ju C, Kong D, Lee Y, Ge G, Song Y, Liu J, Kwak JM. Methionine synthase 1 provides methionine for activation of the GLR3.5 Ca2+ channel and regulation of germination in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:178-187. [PMID: 31563952 PMCID: PMC6913737 DOI: 10.1093/jxb/erz431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 09/11/2019] [Indexed: 05/09/2023]
Abstract
Seed germination is a developmental process regulated by numerous internal and external cues. Our previous studies have shown that calcium influx mediated by the Arabidopsis glutamate receptor homolog 3.5 (AtGLR3.5) modulates the expression of the ABSCISIC ACID INSENSITIVE 4 (ABI4) transcription factor during germination and that L-methionine (L-Met) activates AtGLR3.1/3.5 Ca2+ channels in guard cells. However, it is not known whether L-Met participates in regulation of germination and what cellular mechanism is responsible for Met production during germination. Here, we describe Arabidopsis methionine synthase 1 (AtMS1), which acts in the final step of Met biosynthesis, synthesizes the Met required for the activation of AtGLR3.5 Ca2+ channels whose expression is up-regulated during germination, leading to the regulation of seed germination. We show that exogenous L-Met promotes germination in an AtGRL3.5-dependent manner. We also demonstrate that L-Met directly regulates the AtGLR3.5-mediated increase in cytosolic Ca2+ level in seedlings. We provide pharmacological and genetic evidence that Met synthesized via AtMS1 acts upstream of the AtGLR3.5-mediated Ca2+ signal and regulates the expression of ABI4, a major regulator in the abscisic acid response in seeds. Overall, our results link AtMS1, L-Met, the AtGLR3.5 Ca2+ channel, Ca2+ signals, and ABI4, and shed light on the physiological role and molecular mechanism of L-Met in germination.
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Affiliation(s)
- Chuanli Ju
- College of Life Sciences, Capital Normal University, Beijing, China
- Correspondence: or
| | - Dongdong Kong
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Yuree Lee
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Gege Ge
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Yanan Song
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Jiawen Liu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - June M Kwak
- Department of New Biology, DGIST, Daegu, Republic of Korea
- Correspondence: or
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Nanda AK, El Habti A, Hocart CH, Masle J. ERECTA receptor-kinases play a key role in the appropriate timing of seed germination under changing salinity. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6417-6435. [PMID: 31504732 PMCID: PMC6859730 DOI: 10.1093/jxb/erz385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/15/2019] [Indexed: 05/21/2023]
Abstract
Appropriate timing of seed germination is crucial for the survival and propagation of plants, and for crop yield, especially in environments prone to salinity or drought. However, the exact mechanisms by which seeds perceive changes in soil conditions and integrate them to trigger germination remain elusive, especially once the seeds are non-dormant. In this study, we determined that the Arabidopsis ERECTA (ER), ERECTA-LIKE1 (ERL1), and ERECTA-LIKE2 (ERL2) leucine-rich-repeat receptor-like kinases regulate seed germination and its sensitivity to changes in salt and osmotic stress levels. Loss of ER alone, or in combination with ERL1 and/or ERL2, slows down the initiation of germination and its progression to completion, or arrests it altogether under saline conditions, until better conditions return. This function is maternally controlled via the tissues surrounding the embryo, with a primary role being played by the properties of the seed coat and its mucilage. These relate to both seed-coat expansion and subsequent differentiation and to salinity-dependent interactions between the mucilage, subtending seed coat layers and seed interior in the germinating seed. Salt-hypersensitive er105, er105 erl1.2, er105 erl2.1 and triple-mutant seeds also exhibit increased sensitivity to exogenous ABA during germination, and under salinity show an enhanced up-regulation of the germination repressors and inducers of dormancy ABA-insensitive-3, ABA-insensitive-5, DELLA-encoding RGL2, and Delay-Of-Germination-1. These findings reveal a novel role of the ERECTA receptor-kinases in the sensing of conditions at the seed surface and the integration of developmental, dormancy and stress signalling pathways in seeds. They also open novel avenues for the genetic improvement of plant adaptation to changing drought and salinity patterns.
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Affiliation(s)
- Amrit K Nanda
- Research School of Biology, The Australian National University, Canberra ACT, Australia
| | - Abdeljalil El Habti
- Research School of Biology, The Australian National University, Canberra ACT, Australia
| | - Charles H Hocart
- Research School of Biology, The Australian National University, Canberra ACT, Australia
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63
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Qu C, Zhao H, Chen J, Zuo Z, Sun X, Huang J, Yang C, Zhang X, Zhang P, Quan X, Xu Z, Liu G. The transcriptional events and their relationship to physiological changes during poplar seed germination and post-germination. BMC Genomics 2019; 20:801. [PMID: 31684868 PMCID: PMC6829952 DOI: 10.1186/s12864-019-6180-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background Seed germination, the foundation of plant propagation, involves a series of changes at the molecular level. Poplar is a model woody plant, but the molecular events occurring during seed germination in this species are unclear. Results In this study, we investigated changes in gene transcriptional levels during different germination periods in poplar by high-throughput sequencing technology. Analysis of genes expressed at specific germination stages indicated that these genes are distributed in many metabolic pathways. Enrichment analysis of significantly differentially expressed genes based on hypergeometric testing revealed that multiple pathways, such as pathways related to glycolysis, lipid, amino acid, protein and ATP synthesis metabolism, changed significantly at the transcriptional level during seed germination. A comparison of ΣZ values uncovered a series of transcriptional changes in biological processes related to primary metabolism during poplar seed germination. Among these changes, genes related to CHO metabolism were the first to be activated, with subsequent expression of genes involved in lipid metabolism and then those associated with protein metabolism. The pattern of metabolomic and physiological index changes further verified the sequence of some biological events. Conclusions Our study revealed molecular events occurring at the transcriptional level during seed germination and determined their order. These events were further verified by patterns of changes of metabolites and physiological indexes. Our findings lay a foundation for the elucidation of the molecular mechanisms responsible for poplar seed germination.
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Affiliation(s)
- Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Hancheng Zhao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jinyuan Chen
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhuang Zuo
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xue Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jiahuan Huang
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Chengjun Yang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xiuli Zhang
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Peng Zhang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xiankui Quan
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.,College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China. .,School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
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64
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Sergeant K, Printz B, Guerriero G, Renaut J, Lutts S, Hausman JF. The Dynamics of the Cell Wall Proteome of Developing Alfalfa Stems. BIOLOGY 2019; 8:E60. [PMID: 31430995 PMCID: PMC6784106 DOI: 10.3390/biology8030060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/06/2019] [Accepted: 08/14/2019] [Indexed: 12/24/2022]
Abstract
In this study, the cell-wall-enriched subproteomes at three different heights of alfalfa stems were compared. Since these three heights correspond to different states in stem development, a view on the dynamics of the cell wall proteome during cell maturation is obtained. This study of cell wall protein-enriched fractions forms the basis for a description of the development process of the cell wall and the linking cell wall localized proteins with the evolution of cell wall composition and structure. The sequential extraction of cell wall proteins with CaCl2, EGTA, and LiCl-complemented buffers was combined with a gel-based proteome approach and multivariate analysis. Although the highest similarities were observed between the apical and intermediate stem regions, the proteome patterns are characteristic for each region. Proteins that bind carbohydrates and have proteolytic activity, as well as enzymes involved in glycan remobilization, accumulate in the basal stem region. Beta-amylase and ferritin likewise accumulate more in the basal stem segment. Therefore, remobilization of nutrients appears to be an important process in the oldest stem segment. The intermediate and apical regions are sites of cell wall polymer remodeling, as suggested by the high abundance of proteins involved in the remodeling of the cell wall, such as xyloglucan endoglucosylase, beta-galactosidase, or the BURP-domain containing polygalacturonase non-catalytic subunit. However, the most striking change between the different stem parts is the strong accumulation of a DUF642-conserved domain containing protein in the apical region of the stem, which suggests a particular role of this protein during the early development of stem tissues.
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Affiliation(s)
- Kjell Sergeant
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg.
| | - Bruno Printz
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
- Groupe de Recherche en Physiologie végétale (GRPV), Université catholique de Louvain, Earth and Life Institute Agronomy (ELI-A), 1348 Louvain-la-Neuve, Belgium
| | - Gea Guerriero
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
| | - Jenny Renaut
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
| | - Stanley Lutts
- Groupe de Recherche en Physiologie végétale (GRPV), Université catholique de Louvain, Earth and Life Institute Agronomy (ELI-A), 1348 Louvain-la-Neuve, Belgium
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
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65
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A Weighted Mean Value Analysis to Identify Biological Pathway Activity Changes during Poplar Seed Germination. FORESTS 2019. [DOI: 10.3390/f10080664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Poplar (Populus × xiaohei T. S. Hwang et Liang) is an excellent model plant, with a known genome sequence, for studying woody plant developmental processes, such as seed germination. Here, we report the transcriptional profiling of poplar seeds at five germination stages using RNA-Seq technology. We focused on identifying biological pathway activity changes during seed germination and transcription factors that play important roles in different stages. Among the 16 significantly changing clusters obtained using the STEM method, transcription was significantly enriched in five different clusters, 8, 21, 25, 27, and 35. The oxidative phosphorylation-related genes were only enriched in cluster 9, and expression patterns decreased in 6 and 24 HAI, while ubiquitin-dependent protein catabolic processes were only enriched in cluster 16, and expression patterns increased in 6 HAI. A weighted mean method analysis determined that most primary metabolism-associated categories, such as major carbohydrate metabolism, glycolysis, oxidative pentose phosphate, tricarboxylic acid cycle, lipid metabolism, nucleotide metabolism, amino acid metabolism, and protein metabolism, were elevated between 6 and 48 h after imbibition (HAI). ATP synthesis and C1 metabolism had highly active expression patterns between 0.75 and 48 HAI. The photosynthesis category-associated genes that were identified appeared highly active at 144 HAI. The homogenization of transcription factors in each cluster revealed that the HAP2, C3H zinc finger family, and C2C2(Zn) GATA transcription factors were present in relatively high numbers in cluster 8, while HAP5, Zn-finger (CCHC), FHA, and E2F/DP transcription factor families, as well as SNF7, were present in high numbers in cluster 25. Thus, we identified a series of biological pathway activity changes that occur, and transcription factors that are active, during poplar seed germination. Moreover, this study provides an integrated view of transcriptional regulation that can reveal the molecular events occurring during seed germination.
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66
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Medium-Throughput RNA In Situ Hybridization of Serial Sections from Paraffin-Embedded Tissue Microarrays. Methods Mol Biol 2019. [PMID: 30945181 DOI: 10.1007/978-1-4939-9045-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
(m)RNA spatiotemporal pattern of distribution is of key importance to decipher gene function. In this post-genomic era, numerous transcriptomic studies are made publicly available, sometimes reaching a tissular resolution and even more rarely the cellular level. This "one tissue-numerous genes" information can be completed by the reverse "one gene-numerous tissues" picture through traditional RNA in situ hybridization (ISH). Here, we present a method including (1) principles of transcriptomic data mining to be performed prior and following ISH and (2) a detailed step-by-step medium-throughput ISH protocol performed on serial sections from tissue microarrays. In a recent work, we implemented this method for 39 selected genes studied by medium-throughput ISH complementing an existing tissue-specific transcriptomic dataset focused on the model plant Arabidopsis seed development kinetics (Francoz et al., Scientific Reports 6:24644, 2016). This full integration of ISH and transcriptomics demonstrated the complementarity of both techniques in terms of tissue/cell specificity, signal sensitivity, gene specificity, and spatiotemporal resolution.
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67
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Footitt S, Clewes R, Feeney M, Finch‐Savage WE, Frigerio L. Aquaporins influence seed dormancy and germination in response to stress. PLANT, CELL & ENVIRONMENT 2019; 42:2325-2339. [PMID: 30986891 PMCID: PMC6767449 DOI: 10.1111/pce.13561] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/09/2019] [Indexed: 05/10/2023]
Abstract
Aquaporins influence water flow in plants, yet little is known of their involvement in the water-driven process of seed germination. We therefore investigated their role in seeds in the laboratory and under field and global warming conditions. We mapped the expression of tonoplast intrinsic proteins (TIPs) during dormancy cycling and during germination under normal and water stress conditions. We found that the two key tonoplast aquaporins, TIP3;1 and TIP3;2, which have previously been implicated in water or solute transport, respectively, act antagonistically to modulate the response to abscisic acid, with TIP3;1 being a positive and TIP3;2 a negative regulator. A third isoform, TIP4;1, which is normally expressed upon completion of germination, was found to play an earlier role during water stress. Seed TIPs also contribute to the regulation of depth of primary dormancy and differences in the induction of secondary dormancy during dormancy cycling. Protein and gene expression during annual cycling under field conditions and a global warming scenario further illustrate this role. We propose that the different responses of the seed TIP contribute to mechanisms that influence dormancy status and the timing of germination under variable soil conditions.
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Affiliation(s)
- Steven Footitt
- School of Life SciencesUniversity of WarwickWarwickshireCV4 7ALUK
| | - Rachel Clewes
- School of Life SciencesUniversity of WarwickWarwickshireCV4 7ALUK
| | - Mistianne Feeney
- School of Life SciencesUniversity of WarwickWarwickshireCV4 7ALUK
| | | | - Lorenzo Frigerio
- School of Life SciencesUniversity of WarwickWarwickshireCV4 7ALUK
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68
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Ponnaiah M, Gilard F, Gakière B, El-Maarouf-Bouteau H, Bailly C. Regulatory actors and alternative routes for Arabidopsis seed germination are revealed using a pathway-based analysis of transcriptomic datasets. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:163-175. [PMID: 30868664 DOI: 10.1111/tpj.14311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/07/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
Regulation of seed germination by dormancy relies on a complex network of transcriptional and post-transcriptional modifications during seed imbibition that controls seed adaptive responses to environmental cues. High-throughput technologies have brought significant progress in the understanding of this phenomenon and have led to identify major regulators of seed germination, mostly by studying the behaviour of highly differentially expressed genes. However, the actual models of transcriptome analysis cannot catch additive effects of small variations of gene expression in individual signalling or metabolic pathways, which are also likely to control germination. Therefore, the comprehension of the molecular mechanism regulating germination is still incomplete and to gain knowledge about this process we have developed a pathway-based analysis of transcriptomic Arabidopsis datasets, to identify regulatory actors of seed germination. The method allowed quantifying the level of deregulation of a wide range of pathways in dormant versus non-dormant seeds. Clustering pathway deregulation scores of germinating and dormant seed samples permitted the identification of mechanisms involved in seed germination such as RNA transport or vitamin B6 metabolism, for example. Using this method, which was validated by metabolomics analysis, we also demonstrated that Col and Cvi seeds follow different metabolic routes for completing germination, demonstrating the genetic plasticity of this process. We finally provided an extensive basis of analysed transcriptomic datasets that will allow further identification of mechanisms controlling seed germination.
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Affiliation(s)
- Maharajah Ponnaiah
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, F-75005, Paris, France
| | - Françoise Gilard
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université d'Evry, Université Paris-Diderot, Université Paris-Sud, Sorbonne Paris-Cité, Saclay Plant Sciences, Orsay, France
| | - Bertrand Gakière
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université d'Evry, Université Paris-Diderot, Université Paris-Sud, Sorbonne Paris-Cité, Saclay Plant Sciences, Orsay, France
| | | | - Christophe Bailly
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, F-75005, Paris, France
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69
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Qu C, Zuo Z, Cao L, Huang J, Sun X, Zhang P, Yang C, Li L, Xu Z, Liu G. Comprehensive dissection of transcript and metabolite shifts during seed germination and post-germination stages in poplar. BMC PLANT BIOLOGY 2019; 19:279. [PMID: 31242858 PMCID: PMC6595626 DOI: 10.1186/s12870-019-1862-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/31/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND Seed germination, a complex, physiological-morphogenetic process, is a critical stage in the life cycle of plants. Biological changes in germinating seeds have not been investigated in poplar, a model woody plant. RESULTS In this study, we exploited next-generation sequencing and metabolomics analysis and uncovered a series of significantly different genes and metabolites at various stages of seed germination and post germination. The K-means method was used to identify multiple transcription factors, including AP2/EREBP, DOF, and YABBY, involved in specific seed germination and post-germination stages. A weighted gene coexpression network analysis revealed that cell wall, amino acid metabolism, and transport-related pathways were significantly enriched during stages 3 and 5, with no significant enrichment observed in primary metabolic processes such as glycolysis and the tricarboxylic acid cycle. A metabolomics analysis detected significant changes in intermediate metabolites in these primary metabolic processes, while a targeted correlation network analysis identified the gene family members most relevant to these changing metabolites. CONCLUSIONS Taken together, our results provide important insights into the molecular networks underlying poplar seed germination and post-germination processes. The targeted correlation network analysis approach developed in this study can be applied to search for key candidate genes in specific biochemical reactions and represents a new strategy for joint multiomics analyses.
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Affiliation(s)
- Chunpu Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhuang Zuo
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Lina Cao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jiahuan Huang
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xue Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Peng Zhang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Chengjun Yang
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Lixin Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
- College of Life Science, Northeast Forestry University, Harbin, 150040, People's Republic of China.
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
- School of Forestry, Northeast Forestry University, Harbin, 150040, People's Republic of China.
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70
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Bafoil M, Le Ru A, Merbahi N, Eichwald O, Dunand C, Yousfi M. New insights of low-temperature plasma effects on germination of three genotypes of Arabidopsis thaliana seeds under osmotic and saline stresses. Sci Rep 2019; 9:8649. [PMID: 31209339 PMCID: PMC6572809 DOI: 10.1038/s41598-019-44927-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/28/2019] [Indexed: 11/29/2022] Open
Abstract
In order to investigate the effects of low temperature plasmas on germination of Arabidopsis thaliana seeds, a dielectric barrier discharge device generating the plasma in ambient air was used. To highlight the different plasma effects on the seed surface, saline and osmotic stresses were considered in the case of reference Col-0 seeds and two further seed coat mutants gl2 and gpat5 to better analyse the seed surface changes and their consequences on germination. The GL2 gene encode a transcription factor controlling the balance between the biosynthesis of fatty acids in the embryo and the production of mucilage and flavonoid pigments in the seed coat. The GPAT5 gene encode for an acyltransferase necessary for the accumulation of suberin in the seed coat which is essential for the embryo protection. The testa and endosperm ruptures are identified to note the germination stage. An increasing of germination rate, possibly due to the modification of mantle layers structure, is observed in most of cases, even in presence of saline or osmotic stress, after plasma treatment. Furthermore, we demonstrated that the germination rate of the gl2 mutant seeds is increased by at most 47% after plasma treatment, contrariwise, the germination of gpat5 mutant being initially lower is inhibited by the same plasma treatment. The scanning electron microscopy pictures and confocal microscopy fluorescence both showed changes of the exterior aspects of the seeds after plasma treatment. Considering these results, we assumed that lipid compounds can be found on the surface. To validate this hypothesis, permeability tests were performed, and it was clearly shown that a permeability decrease is induced by the low temperature plasma treatment.
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Affiliation(s)
- Maxime Bafoil
- LAPLACE, UMR CNRS 5213, Université Paul Sabatier, Toulouse, France.,LRSV, UMR CNRS 5546, Université Paul Sabatier, Castanet-Tolosan, France
| | - Aurélie Le Ru
- Fédération de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, Castanet-Tolosan, France
| | - Nofel Merbahi
- LAPLACE, UMR CNRS 5213, Université Paul Sabatier, Toulouse, France
| | - Olivier Eichwald
- LAPLACE, UMR CNRS 5213, Université Paul Sabatier, Toulouse, France
| | - Christophe Dunand
- LRSV, UMR CNRS 5546, Université Paul Sabatier, Castanet-Tolosan, France.
| | - Mohammed Yousfi
- LAPLACE, UMR CNRS 5213, Université Paul Sabatier, Toulouse, France.
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71
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Niazi AK, Delannoy E, Iqbal RK, Mileshina D, Val R, Gabryelska M, Wyszko E, Soubigou-Taconnat L, Szymanski M, Barciszewski J, Weber-Lotfi F, Gualberto JM, Dietrich A. Mitochondrial Transcriptome Control and Intercompartment Cross-Talk During Plant Development. Cells 2019; 8:E583. [PMID: 31200566 PMCID: PMC6627697 DOI: 10.3390/cells8060583] [Citation(s) in RCA: 5] [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: 03/21/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 01/17/2023] Open
Abstract
We address here organellar genetic regulation and intercompartment genome coordination. We developed earlier a strategy relying on a tRNA-like shuttle to mediate import of nuclear transgene-encoded custom RNAs into mitochondria in plants. In the present work, we used this strategy to drive trans-cleaving hammerhead ribozymes into the organelles, to knock down specific mitochondrial RNAs and analyze the regulatory impact. In a similar approach, the tRNA mimic was used to import into mitochondria in Arabidopsis thaliana the orf77, an RNA associated with cytoplasmic male sterility in maize and possessing sequence identities with the atp9 mitochondrial RNA. In both cases, inducible expression of the transgenes allowed to characterise early regulation and signaling responses triggered by these respective manipulations of the organellar transcriptome. The results imply that the mitochondrial transcriptome is tightly controlled by a "buffering" mechanism at the early and intermediate stages of plant development, a control that is released at later stages. On the other hand, high throughput analyses showed that knocking down a specific mitochondrial mRNA triggered a retrograde signaling and an anterograde nuclear transcriptome response involving a series of transcription factor genes and small RNAs. Our results strongly support transcriptome coordination mechanisms within the organelles and between the organelles and the nucleus.
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Affiliation(s)
- Adnan Khan Niazi
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, Pakistan.
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France.
| | - Rana Khalid Iqbal
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Daria Mileshina
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Romain Val
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Marta Gabryelska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Eliza Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France.
| | - Maciej Szymanski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, A. Mickiewicz University Poznan, Ul. Umultowska 89, 61-614 Poznan, Poland.
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
- NanoBioMedical Centre of the Adam Mickiewicz University, Umultowska 85, 61614 Poznan, Poland.
| | - Frédérique Weber-Lotfi
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - José Manuel Gualberto
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - André Dietrich
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
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Nonogaki H. Seed germination and dormancy: The classic story, new puzzles, and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:541-563. [PMID: 30565406 DOI: 10.1111/jipb.12762] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/17/2018] [Indexed: 05/18/2023]
Abstract
This review highlights recent progresses in seed germination and dormancy research. Research on the weakening of the endosperm during germination, which is almost a classic theme in seed biology, was resumed by α-xylosidase studies. Strong genetic evidence was presented to suggest that the quality control of xyloglucan biosynthesis in the endosperm (and the embryo) plays a critical role in germination. Further analyses on the endosperm and the adjacent layers have suggested that the cutin coat in the endosperm-testa interphase negatively affects germination while the endosperm-embryo interphase produces a sheath that facilitates germination. These progresses significantly advanced our understanding of seed germination mechanisms. A breakthrough in dormancy research, on the other hand, revealed the unique abscisic acid signaling pathway that is regulated by DELAY OF GERMINATION1 (DOG1). The detailed analysis of DOG1 expression uncovered the intriguing story of reciprocal regulation of the sense-antisense pair, which generated new questions. Recent studies also suggested that the DOG1 function is not limited to dormancy but extended through general seed maturation, which provokes questions about the evolution of DOG1 family proteins. Seed biology is becoming more exciting with the classic stories being revitalized and new puzzles emerging from the frontier.
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73
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Sánchez-Montesino R, Bouza-Morcillo L, Marquez J, Ghita M, Duran-Nebreda S, Gómez L, Holdsworth MJ, Bassel G, Oñate-Sánchez L. A Regulatory Module Controlling GA-Mediated Endosperm Cell Expansion Is Critical for Seed Germination in Arabidopsis. MOLECULAR PLANT 2019; 12:71-85. [PMID: 30419294 PMCID: PMC7086157 DOI: 10.1016/j.molp.2018.10.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 05/19/2023]
Abstract
A key component of seed germination is the interplay of mechanical forces governing embryo growth and the surrounding restraining endosperm tissue. Endosperm cell separation is therefore thought to play a critical role in the control of this developmental transition. Here we demonstrate that in Arabidopsis thaliana seeds, endosperm cell expansion is a key component of germination. Endosperm cells expand to accommodate embryo growth prior to germination. We show that this is an actively regulated process supported by spatiotemporal control of the cell expansion gene EXPANSIN 2 (EXPA2). The NAC transcription factors NAC25 and NAC1L were identified as upstream regulators of EXPA2 expression, gibberellin-mediated endosperm expansion, and seed germination. The DELLA protein RGL2 repressed activation of the EXPA2 promoter by NAC25/NAC1L. Taken together, our findings uncover a key role of the GA/DELLA-NAC25/NAC1L-EXPA2 network in regulating endosperm cell expansion to control the seed-to-seedling transition.
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Affiliation(s)
- Rocío Sánchez-Montesino
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
| | - Laura Bouza-Morcillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
| | - Julietta Marquez
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Melania Ghita
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | | | - Luis Gómez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain; Departamento de Sistemas y Recursos Naturales, E.T.S.I. Montes, Forestal y del Medio Natural, Campus de Moncloa, 28040 Madrid, Spain
| | | | - George Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Luis Oñate-Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain.
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74
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Pluskota WE, Pupel P, Głowacka K, Okorska SB, Jerzmanowski A, Nonogaki H, Górecki RJ. Jasmonic acid and ethylene are involved in the accumulation of osmotin in germinating tomato seeds. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:74-81. [PMID: 30537615 DOI: 10.1016/j.jplph.2018.11.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/15/2018] [Accepted: 11/17/2018] [Indexed: 05/18/2023]
Abstract
The expression of SlNP24 encoding osmotin was studied in germinating tomato seeds Solanum lycopersicum L. cv. Moneymaker. The results show that the accumulation of the transcripts of SlNP24 and its potential upstream regulator TERF1 encoding an ethylene response factor was induced by ethylene and methyl jasmonate in germinating tomato seeds. There was no effect of gibberellins on the expression of the genes studied. The expression of SlNP24 was localized in the micropylar region of the endosperm of tomato seeds. The promoter of tomato osmotin was active in the endosperm cells of transgenic Arabidopsis thaliana seeds, which contain reporter genes under control of SlNP24 promoter. The activity of SlNP24 promoter in A. thaliana reporter line seeds was visible when the expression of its ortholog gene in A. thaliana (AtOMS34) was observed. The mechanism of induction and a possible role of NP24 in germinating tomato seeds are discussed.
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Affiliation(s)
- Wioletta E Pluskota
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-718 Olsztyn, Poland.
| | - Piotr Pupel
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-718 Olsztyn, Poland
| | - Katarzyna Głowacka
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-718 Olsztyn, Poland
| | - Sylwia B Okorska
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-718 Olsztyn, Poland
| | - Andrzej Jerzmanowski
- Warsaw University and Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Hiroyuki Nonogaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Ryszard J Górecki
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-718 Olsztyn, Poland
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75
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Wang L, Waters MT, Smith SM. Karrikin-KAI2 signalling provides Arabidopsis seeds with tolerance to abiotic stress and inhibits germination under conditions unfavourable to seedling establishment. THE NEW PHYTOLOGIST 2018; 219:605-618. [PMID: 29726620 DOI: 10.1111/nph.15192] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/27/2018] [Indexed: 05/06/2023]
Abstract
The control of seed germination in response to environmental conditions is important for plant success. We investigated the role of the karrikin receptor KARRIKIN INSENSITIVE2 (KAI2) in the response of Arabidopsis seeds to osmotic stress, salinity and high temperature. Germination of the kai2 mutant was examined in response to NaCl, mannitol and elevated temperature. The effect of karrikin on germination of wild-type seeds, hypocotyl elongation and the expression of karrikin-responsive genes was also examined in response to such stresses. The kai2 seeds germinated less readily than wild-type seeds and germination was more sensitive to inhibition by abiotic stress. Karrikin-induced KAI2 signalling stimulated germination of wild-type seeds under favourable conditions, but, surprisingly, inhibited germination in the presence of osmolytes or at elevated temperature. By contrast, GA stimulated germination of wild-type seeds and mutants under all conditions. Karrikin induced expression of DLK2 and KUF1 genes and inhibited hypocotyl elongation independently of osmotic stress. Under mild osmotic stress, karrikin enhanced expression of DREB2A, WRKY33 and ERF5 genes, but not ABA signalling genes. Thus, the karrikin-KAI2 signalling system can protect against abiotic stress, first by providing stress tolerance, and second by inhibiting germination under conditions unfavourable to seedling establishment.
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Affiliation(s)
- Lu Wang
- School of Natural Sciences, University of Tasmania, Tasmania, 7001, Australia
| | - Mark T Waters
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, 6009, Australia
| | - Steven M Smith
- School of Natural Sciences, University of Tasmania, Tasmania, 7001, Australia
- Institute of Genetics and Developmental Biology, Chinese Academy of sciences, Beijing, 100101, China
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76
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Bafoil M, Jemmat A, Martinez Y, Merbahi N, Eichwald O, Dunand C, Yousfi M. Effects of low temperature plasmas and plasma activated waters on Arabidopsis thaliana germination and growth. PLoS One 2018; 13:e0195512. [PMID: 29630641 PMCID: PMC5891017 DOI: 10.1371/journal.pone.0195512] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/23/2018] [Indexed: 11/18/2022] Open
Abstract
Two plasma devices at atmospheric pressure (air dielectric barrier discharge and helium plasma jet) have been used to study the early germination of Arabidopsis thaliana seeds during the first days. Then, plasma activated waters are used during the later stage of plant development and growth until 42 days. The effects on both testa and endospserm ruptures during the germination stage are significant in the case of air plasma due to its higher energy and efficiency of producing reactive oxygen species than the case of helium plasma. The latter has shown distinct effects only for testa rupture. Analysis of germination stimulations are based on specific stainings for reactive oxygen species production, peroxidase activity and also membrane permeability tests. Furthermore, scanning electron microscopy (SEM) has shown a smoother seed surface for air plasma treated seeds that can explain the plasma induced-germination. During the growth stage, plants were watered using 4 kinds of water (tap and deionized waters activated or not by the low temperature plasma jet). With regards to other water kinds, the characterization of the tap water has shown a larger conductivity, acidity and concentration of reactive nitrogen and oxygen species. Only the tap water activated by the plasma jet has shown a significant effect on the plant growth. This effect could be correlated to reactive nitrogen species such as nitrite/nitrate species present in plasma activated tap water.
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Affiliation(s)
- Maxime Bafoil
- LAPLACE, UMR CNRS 5213, Université Paul Sabatier, Toulouse, France
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville, Castanet Tolosan, France
| | - Achraf Jemmat
- LAPLACE, UMR CNRS 5213, Université Paul Sabatier, Toulouse, France
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville, Castanet Tolosan, France
| | - Yves Martinez
- Fédération de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, Castanet-Tolosan, France
| | - Nofel Merbahi
- LAPLACE, UMR CNRS 5213, Université Paul Sabatier, Toulouse, France
| | - Olivier Eichwald
- LAPLACE, UMR CNRS 5213, Université Paul Sabatier, Toulouse, France
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville, Castanet Tolosan, France
- * E-mail: (MY); (CD)
| | - Mohammed Yousfi
- LAPLACE, UMR CNRS 5213, Université Paul Sabatier, Toulouse, France
- * E-mail: (MY); (CD)
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77
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Wakeel A, Ali I, Khan AR, Wu M, Upreti S, Liu D, Liu B, Gan Y. Involvement of histone acetylation and deacetylation in regulating auxin responses and associated phenotypic changes in plants. PLANT CELL REPORTS 2018; 37:51-59. [PMID: 28948334 DOI: 10.1007/s00299-017-2205-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/05/2017] [Indexed: 05/04/2023]
Abstract
The most recent outcomes about the transcription factors and transcription complexes mediated auxin signaling pathway by the histone acetylation and deacetylation. The phytohormone auxin, is required to regulate its accumulation spatiotemporally and responses to orchestrate various developmental levels in plants. Histone acetylation and deacetylation modulate auxin biosynthesis, its distribution and accumulation. In the absence of auxin, histone deacetylase represses the expression of auxin-responsive genes. Various transcription factors and transcription complexes facilitate the proper regulation of auxin signaling pathway genes. The primary and lateral root development, promotion of flowering and initiation of seed germination are all regulated by auxin-mediated histone acetylation and deacetylation. These findings conclude the auxin mode of action, which is mediated by histone acetylation and deacetylation, and associated phenotypic responses in plants, along with the underlying mechanism of these modifications.
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Affiliation(s)
- Abdul Wakeel
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Imran Ali
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ali Raza Khan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Minjie Wu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sakila Upreti
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Dongdong Liu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Bohan Liu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yinbo Gan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
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78
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Murgia I, Morandini P. Iron Deficiency Prolongs Seed Dormancy in Arabidopsis Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:2077. [PMID: 29276522 PMCID: PMC5727067 DOI: 10.3389/fpls.2017.02077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/21/2017] [Indexed: 05/21/2023]
Abstract
The understanding of seed dormancy, germination and longevity are important goals in plant biology, with relevant applications for agriculture, food industry and also human nutrition. Reactive Oxygen Species (ROS) are key molecules involved in the release of dormancy, when their concentrations fall within the so called 'oxidative window.' The mechanisms of ROS distribution and sensing in seeds, from dormant to germinating ones, still need elucidation. Also, the impact of iron (Fe) deficiency on seed dormancy is still unexplored; this is surprising, given the known pro-oxidant role of Fe when in a free form. We provide evidence of a link between plant Fe nutrition and dormancy of progeny seeds by using different Arabidopsis ecotypes and mutants with different dormancy strengths grown in control soil or under severe Fe deficiency. The latter condition extends the dormancy in several genotypes. The focus on the mechanisms involved in the Fe deficiency-dependent alteration of dormancy and longevity promises to be a key issue in seed (redox) biology.
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Affiliation(s)
- Irene Murgia
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
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79
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Lin H, Yu J, Pearce SP, Zhang D, Wilson ZA. RiceAntherNet: a gene co-expression network for identifying anther and pollen development genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1076-1091. [PMID: 29031031 DOI: 10.1111/tpj.13744] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 06/07/2023]
Abstract
In plants, normal anther and pollen development involves many important biological events and complex molecular regulatory coordination. Understanding gene regulatory relationships during male reproductive development is essential for fundamental biology and crop breeding. In this work, we developed a rice gene co-expression network for anther development (RiceAntherNet) that allows prediction of gene regulatory relationships during pollen development. RiceAntherNet was generated from 57 rice anther tissue microarrays across all developmental stages. The microarray datasets from nine rice male sterile mutants, including msp1-4, ostdl1a, gamyb-2, tip2, udt1-1, tdr, eat1-1, ptc1 and mads3-4, were used to explore and test the network. Among the changed genes, three clades showing differential expression patterns were constructed to identify genes associated with pollen formation. Many of these have known roles in pollen development, for example, seven genes in Clade 1 (OsABCG15, OsLAP5, OsLAP6, DPW, CYP703A3, OsNP1 and OsCP1) are involved in rice pollen wall formation. Furthermore, Clade 1 contained 12 genes whose predicted orthologs in Arabidopsis have been reported as key during pollen development and may play similar roles in rice. Genes in Clade 2 are expressed earlier than Clade 1 (anther stages 2-9), while genes in Clade 3 are expressed later (stages 10-12). RiceAntherNet serves as a valuable tool for identifying novel genes during plant anther and pollen development. A website is provided (https://www.cpib.ac.uk/anther/riceindex.html) to present the expression profiles for gene characterization. This will assist in determining the key relationships between genes, thus enabling characterization of critical genes associated with anther and pollen regulatory networks.
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Affiliation(s)
- Hong Lin
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Division of Plant & Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, UK
| | - Jing Yu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Simon P Pearce
- School of Mathematics, University of Manchester, Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Dabing Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zoe A Wilson
- Division of Plant & Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, UK
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham, UK
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80
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Cruz-Valderrama JE, Jiménez-Durán K, Zúñiga-Sánchez E, Salazar-Iribe A, Márquez-Guzmán J, Gamboa-deBuen A. Degree of pectin methyl esterification in endosperm cell walls is involved in embryo bending in Arabidopsis thaliana. Biochem Biophys Res Commun 2017; 495:639-645. [PMID: 29137987 DOI: 10.1016/j.bbrc.2017.11.077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 01/24/2023]
Abstract
The endosperm is a transitory structure involved in proper embryo elongation. The cell walls of mature seed endosperm are generally composed of a uniform distribution of cellulose, unesterified homogalacturonans, and arabinans. Recent studies suggest that changes in cell wall properties during endosperm development could be related to embryo growth. The degree of methyl esterification of homogalacturonans may be involved in this endosperm tissue remodelling. The relevance of the degree of homogalacturonan methyl esterification during seed development was determined by immunohistochemical analyses using a panel of probes with specificity for homogalaturonans with different degrees of methyl esterification. Low-esterified and un-esterified homogalacturonans were abundant in endosperm cells during embryo bending and were also detected in mature embryos. BIDXII (BDX) could be involved in seed development, because bdx-1 mutants had misshapen embryos. The methyl esterification pattern described for WT seeds was different during bdx-1 seed development; un-esterified homogalacturonans were scarcely present in the cell walls of endosperm in bending embryos and mature seeds. Our results suggested that the degree of methyl esterification of homogalacturonans in the endosperm cell wall may be involved in proper embryo development.
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Affiliation(s)
- José E Cruz-Valderrama
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP.04510, CDMX, Mexico
| | - Karina Jiménez-Durán
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP.04510, CDMX, Mexico
| | - Esther Zúñiga-Sánchez
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP.04510, CDMX, Mexico
| | - Alexis Salazar-Iribe
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP.04510, CDMX, Mexico
| | - Judith Márquez-Guzmán
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP.04510, CDMX, Mexico
| | - Alicia Gamboa-deBuen
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP.04510, CDMX, Mexico.
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81
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Silva AT, Ligterink W, Hilhorst HWM. Metabolite profiling and associated gene expression reveal two metabolic shifts during the seed-to-seedling transition in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2017; 95:481-496. [PMID: 29046998 PMCID: PMC5688192 DOI: 10.1007/s11103-017-0665-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 10/04/2017] [Indexed: 05/02/2023]
Abstract
Metabolic and transcriptomic correlation analysis identified two distinctive profiles involved in the metabolic preparation for seed germination and seedling establishment, respectively. Transcripts were identified that may control metabolic fluxes. The transition from a quiescent metabolic state (dry seed) to the active state of a vigorous seedling is crucial in the plant's life cycle. We analysed this complex physiological trait by measuring the changes in primary metabolism that occur during the transition in order to determine which metabolic networks are operational. The transition involves several developmental stages from seed germination to seedling establishment, i.e. between imbibition of the mature dry seed and opening of the cotyledons, the final stage of seedling establishment. We hypothesized that the advancement of growth is associated with certain signature metabolite profiles. Metabolite-metabolite correlation analysis underlined two specific profiles which appear to be involved in the metabolic preparation for seed germination and efficient seedling establishment, respectively. Metabolite profiles were also compared to transcript profiles and although transcriptional changes did not always equate to a proportional metabolic response, in depth correlation analysis identified several transcripts that may directly influence the flux through metabolic pathways during the seed-to-seedling transition. This correlation analysis also pinpointed metabolic pathways which are significant for the seed-to-seedling transition, and metabolite contents that appeared to be controlled directly by transcript abundance. This global view of the transcriptional and metabolic changes during the seed-to-seedling transition in Arabidopsis opens up new perspectives for understanding the complex regulatory mechanism underlying this transition.
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Affiliation(s)
- Anderson Tadeu Silva
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA.
| | - Wilco Ligterink
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Henk W M Hilhorst
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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82
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Ma S, Ding Z, Li P. Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. BMC PLANT BIOLOGY 2017; 17:131. [PMID: 28764653 PMCID: PMC5540570 DOI: 10.1186/s12870-017-1077-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/19/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The advent of big data in biology offers opportunities while poses challenges to derive biological insights. For maize, a large amount of publicly available transcriptome datasets have been generated but a comprehensive analysis is lacking. RESULTS We constructed a maize gene co-expression network based on the graphical Gaussian model, using massive RNA-seq data. The network, containing 20,269 genes, assembles into 964 gene modules that function in a variety of plant processes, such as cell organization, the development of inflorescences, ligules and kernels, the uptake and utilization of nutrients (e.g. nitrogen and phosphate), the metabolism of benzoxazionids, oxylipins, flavonoids, and wax, and the response to stresses. Among them, the inflorescences development module is enriched with domestication genes (like ra1, ba1, gt1, tb1, tga1) that control plant architecture and kernel structure, while multiple other modules relate to diverse agronomic traits. Contained within these modules are transcription factors acting as known or potential expression regulators for the genes within the same modules, suggesting them as candidate regulators for related biological processes. A comparison with an established Arabidopsis network revealed conserved gene association patterns for specific modules involved in cell organization, nutrients uptake & utilization, and metabolism. The analysis also identified significant divergences between the two species for modules that orchestrate developmental pathways. CONCLUSIONS This network sheds light on how gene modules are organized between different species in the context of evolutionary divergence and highlights modules whose structure and gene content can provide important resources for maize gene functional studies with application potential.
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Affiliation(s)
- Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui China
| | - Zehong Ding
- The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan China
| | - Pinghua Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong China
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83
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Wen D, Xu H, Xie L, He M, Hou H, Zhang C. A loose endosperm structure of wheat seed produced under low nitrogen level promotes early germination by accelerating water uptake. Sci Rep 2017; 7:3116. [PMID: 28596607 PMCID: PMC5465190 DOI: 10.1038/s41598-017-03333-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/26/2017] [Indexed: 02/01/2023] Open
Abstract
Water uptake is the fundamental requirement for the initiation and completion of seed germination that is a vital phase in the life cycle of seed plants. We found that seeds produced under four nitrogen levels showed significantly different germination speed. The objective of this study was to study the mechanism of rapid seed germination and explore which pathways and genes play critical roles in radicle protrusion. Anatomical data revealed that seed protein content affected endosperm structure of seeds. Moreover, scanning electron microscope maps showed that faster germinated seeds had a looser endosperm structure compared with other seeds. Subsequently, high throughout RNA-seq data were used to compare the transcriptomes of imbibed seeds with different germination speed. Gene ontology (GO) term enrichment analysis revealed that cell wall metabolism related genes significantly up-regulated in faster germinated seeds. In these genes, the top four were chitinase that had about fourfold higher expression in faster germinated seeds. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that faster germinated seeds had enhanced expression in glutathione metabolism. By combining these results, we propose a model for nitrogen fertilizer affects germination speed of wheat seed, which provide new insights into seed germination.
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Affiliation(s)
- Daxing Wen
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China
| | - Haicheng Xu
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China
| | - Liuyong Xie
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China
| | - Mingrong He
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China
| | - Hongcun Hou
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China
| | - Chunqing Zhang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China.
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84
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Bai B, Peviani A, van der Horst S, Gamm M, Snel B, Bentsink L, Hanson J. Extensive translational regulation during seed germination revealed by polysomal profiling. THE NEW PHYTOLOGIST 2017; 214:233-244. [PMID: 27935038 PMCID: PMC5347915 DOI: 10.1111/nph.14355] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/25/2016] [Indexed: 05/18/2023]
Abstract
This work investigates the extent of translational regulation during seed germination. The polysome occupancy of each gene is determined by genome-wide profiling of total mRNA and polysome-associated mRNA. This reveals extensive translational regulation during Arabidopsis thaliana seed germination. The polysome occupancy of thousands of individual mRNAs changes to a large extent during the germination process. Intriguingly, these changes are restricted to two temporal phases (shifts) during germination, seed hydration and germination. Sequence features, such as upstream open reading frame number, transcript length, mRNA stability, secondary structures, and the presence and location of specific motifs correlated with this translational regulation. These features differed significantly between the two shifts, indicating that independent mechanisms regulate translation during seed germination. This study reveals substantial translational dynamics during seed germination and identifies development-dependent sequence features and cis elements that correlate with the translation control, uncovering a novel and important layer of gene regulation during seed germination.
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Affiliation(s)
- Bing Bai
- Department of Molecular Plant PhysiologyUtrecht University3584 CHUtrechtthe Netherlands
- Wageningen Seed LaboratoryLaboratory of Plant PhysiologyWageningen University6708 PBWageningenthe Netherlands
| | - Alessia Peviani
- Theoretical Biology and BioinformaticsUtrecht University3584 CHUtrechtthe Netherlands
| | - Sjors van der Horst
- Wageningen Seed LaboratoryLaboratory of Plant PhysiologyWageningen University6708 PBWageningenthe Netherlands
- Theoretical Biology and BioinformaticsUtrecht University3584 CHUtrechtthe Netherlands
| | - Magdalena Gamm
- Department of Molecular Plant PhysiologyUtrecht University3584 CHUtrechtthe Netherlands
| | - Berend Snel
- Theoretical Biology and BioinformaticsUtrecht University3584 CHUtrechtthe Netherlands
| | - Leónie Bentsink
- Department of Molecular Plant PhysiologyUtrecht University3584 CHUtrechtthe Netherlands
- Wageningen Seed LaboratoryLaboratory of Plant PhysiologyWageningen University6708 PBWageningenthe Netherlands
| | - Johannes Hanson
- Department of Molecular Plant PhysiologyUtrecht University3584 CHUtrechtthe Netherlands
- Umeå Plant Science CentreDepartment of Plant PhysiologyUniversity of UmeåUmeåSE‐901 87Sweden
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85
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Drost HG, Janitza P, Grosse I, Quint M. Cross-kingdom comparison of the developmental hourglass. Curr Opin Genet Dev 2017; 45:69-75. [PMID: 28347942 DOI: 10.1016/j.gde.2017.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/02/2017] [Indexed: 01/01/2023]
Abstract
The developmental hourglass model has its foundations in classic anatomical studies by von Baer and Haeckel. In this context, even the conservation of animal body plans has been explained by evolutionary constraints acting on mid-embryogenic development. Recent studies have shown that developmental hourglass patterns also exist on the transcriptomic level, mirroring the corresponding morphological patterns. The identification of similar patterns in embryonic, post-embryonic, and life cycle spanning transcriptomes in plant and fungus development, however, contradict the notion of a direct coupling between morphological and molecular patterns. To explain the existence of hourglass patterns across kingdoms and developmental processes, we propose the organizational checkpoint model that integrates the developmental hourglass model into a framework of transcriptome switches.
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Affiliation(s)
- Hajk-Georg Drost
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Philipp Janitza
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
| | - Ivo Grosse
- Martin Luther University Halle-Wittenberg, Institute of Computer Science, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany; German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Marcel Quint
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany.
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86
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Basbouss-Serhal I, Pateyron S, Cochet F, Leymarie J, Bailly C. 5' to 3' mRNA Decay Contributes to the Regulation of Arabidopsis Seed Germination by Dormancy. PLANT PHYSIOLOGY 2017; 173:1709-1723. [PMID: 28126845 PMCID: PMC5338662 DOI: 10.1104/pp.16.01933] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/23/2017] [Indexed: 05/20/2023]
Abstract
The regulation of plant gene expression, necessary for development and adaptive responses, relies not only on RNA transcription but also on messenger RNA (mRNA) fate. To understand whether seed germination relies on the degradation of specific subsets of mRNA, we investigated whether the 5' to 3' RNA decay machinery participated in the regulation of this process. Arabidopsis (Arabidopsis thaliana) seeds of exoribonuclease4 (xrn4) and varicose (vcs) mutants displayed distinct dormancy phenotypes. Transcriptome analysis of xrn4-5 and vcs-8 mutant seeds allowed us to identify genes that are likely to play a role in the control of germination. Study of 5' untranslated region features of these transcripts revealed that specific motifs, secondary energy, and GC content could play a role in their degradation by XRN4 and VCS, and Gene Ontology clustering revealed novel actors of seed dormancy and germination. Several specific transcripts identified as being putative targets of XRN4 and VCS in seeds (PECTIN LYASE-LIKE, ASPARTYL PROTEASE, DWD-HYPERSENSITIVE-TO-ABA3, and YELLOW STRIPE-LIKE5) were further studied by reverse genetics, and their functional roles in the germination process were confirmed by mutant analysis. These findings suggest that completion of germination and its regulation by dormancy also depend on the degradation of specific subsets of mRNA.
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Affiliation(s)
- Isabelle Basbouss-Serhal
- Sorbonne Universités, UPMC Université Paris 06, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., F.C., J.L., C.B.)
- Institute of Plant Sciences Paris Saclay IPS2, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France (S.P.); and
- Institute of Plant Sciences Paris Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France (S.P.)
| | - Stéphanie Pateyron
- Sorbonne Universités, UPMC Université Paris 06, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., F.C., J.L., C.B.)
- Institute of Plant Sciences Paris Saclay IPS2, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France (S.P.); and
- Institute of Plant Sciences Paris Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France (S.P.)
| | - Françoise Cochet
- Sorbonne Universités, UPMC Université Paris 06, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., F.C., J.L., C.B.)
- Institute of Plant Sciences Paris Saclay IPS2, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France (S.P.); and
- Institute of Plant Sciences Paris Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France (S.P.)
| | - Juliette Leymarie
- Sorbonne Universités, UPMC Université Paris 06, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., F.C., J.L., C.B.)
- Institute of Plant Sciences Paris Saclay IPS2, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France (S.P.); and
- Institute of Plant Sciences Paris Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France (S.P.)
| | - Christophe Bailly
- Sorbonne Universités, UPMC Université Paris 06, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., F.C., J.L., C.B.);
- Institute of Plant Sciences Paris Saclay IPS2, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France (S.P.); and
- Institute of Plant Sciences Paris Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France (S.P.)
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87
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Souza NM, Topham AT, Bassel GW. Quantitative analysis of the 3D cell shape changes driving soybean germination. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1531-1537. [PMID: 28444249 PMCID: PMC5444477 DOI: 10.1093/jxb/erx048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Seed germination is central to plant establishment and is the starting point for the majority of world agriculture. This transition from seed to seedling has been extensively studied at an organ level, while few studies have examined the cellular events which underlie it. Reports in the model species Arabidopsis have identified a radicle-derived wave of cell expansion underlying the germination process. Whether this spatiotemporal pattern of cell expansion is specific to this model plant or conserved in other species remains unknown. Here we examined the 3D cell anisotropy driving germination in soybean. By examining changes in cell shape at two positions along the length of the axis over time, preferential growth was observed in the portion of the axis closest to the radicle. A gradient of cell size was observed across the cortical cell layers of the soybean axis, and differences in starting cell size translated into differential relative growth rates across cell layers where larger cells showed greater relative growth rates than smaller cells. Differences in cell position-specific cell anisotropy were also observed. These data demonstrate that a radicle-derived growth pattern is present in the crop species soybean, and reveal the presence of a complex cellular organization in this hypocotyl which show cell type-specific anisotropy diving germination.
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Affiliation(s)
- Nátali Maidl Souza
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
- Universidade Estadual de Londrina, Programa de Pós-Graduação em Agronomia, Londrina, Brazil
| | | | - George W Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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88
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Mitchell J, Johnston IG, Bassel GW. Variability in seeds: biological, ecological, and agricultural implications. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:809-817. [PMID: 27784726 DOI: 10.1093/jxb/erw397] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Variability is observed in biology across multiple scales, ranging from populations, individuals, and cells to the molecular components within cells. This review explores the sources and roles of this variability across these scales, focusing on seeds. From a biological perspective, the role and the impact this variability has on seed behaviour and adaptation to the environment is discussed. The consequences of seed variability on agricultural production systems, which demand uniformity, are also examined. We suggest that by understanding the basis and underlying mechanisms of variability in seeds, strategies to increase seed population uniformity can be developed, leading to enhanced agricultural production across variable climatic conditions.
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Affiliation(s)
- Jack Mitchell
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Iain G Johnston
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - George W Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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89
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Chahtane H, Kim W, Lopez-Molina L. Primary seed dormancy: a temporally multilayered riddle waiting to be unlocked. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:857-869. [PMID: 27729475 DOI: 10.1093/jxb/erw377] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Primary seed dormancy is an important adaptive plant trait whereby seed germination is blocked under conditions that would otherwise be favorable for germination. This trait is found in newly produced mature seeds of many species, but not all. Once produced, dry seeds undergo an aging time period, called dry after-ripening, during which they lose primary dormancy and gradually acquire the capacity to germinate when exposed to favorable germination conditions. Primary seed dormancy has been extensively studied not only for its scientific interest but also for its ecological, phenological, and agricultural importance. Nevertheless, the mechanisms underlying primary seed dormancy and its regulation during after-ripening remain poorly understood. Here we review the principal developmental stages where primary dormancy is established and regulated prior to and during seed after-ripening, where it is progressively lost. We attempt to identify and summarize what is known about the molecular and genetic mechanisms intervening over time in each of these stages.
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Affiliation(s)
- Hicham Chahtane
- Department of Plant Biology and Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Woohyun Kim
- Department of Plant Biology and Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Luis Lopez-Molina
- Department of Plant Biology and Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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90
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Finch-Savage WE, Footitt S. Seed dormancy cycling and the regulation of dormancy mechanisms to time germination in variable field environments. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:843-856. [PMID: 28391330 DOI: 10.1093/jxb/erw477] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Many molecular mechanisms that regulate dormancy have been identified individually in controlled laboratory studies. However, little is known about how the seed employs this complex suite of mechanisms during dormancy cycling in the variable environment of the soil seed bank. Nevertheless, this behaviour is essential to ensure germination takes place in a favourable habitat and climate space, and in the correct season for the resulting plant to complete its life cycle. During their time in the soil seed bank, seeds continually adjust their dormancy status by sensing a range of environmental signals. Those related to slow seasonal change (e.g. temperature) are used for temporal sensing to determine the time of year and depth of dormancy. This alters their sensitivity to signals related to their spatial environment (e.g. light, nitrate, and water potential) that indicate that conditions are suitable for germination, and so trigger the termination of dormancy. We review work on the physiological, molecular, and ecological aspects of seed dormancy in Arabidopsis and interpret it in the context of dormancy cycling in the soil seed bank. This approach has provided new insight into the co-ordination of mechanisms and signalling networks, and the multidimensional sensing that regulates dormancy cycling in a variable environment.
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Affiliation(s)
- William E Finch-Savage
- School of Life Sciences, Wellesbourne Campus, University of Warwick, Warwickshire CV35 9EF, UK
| | - Steven Footitt
- School of Life Sciences, Wellesbourne Campus, University of Warwick, Warwickshire CV35 9EF, UK
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91
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Wei S, Ma X, Pan L, Miao J, Fu J, Bai L, Zhang Z, Guan Y, Mo C, Huang H, Chen M. Transcriptome Analysis of Taxillusi chinensis (DC.) Danser Seeds in Response to Water Loss. PLoS One 2017; 12:e0169177. [PMID: 28046012 PMCID: PMC5207531 DOI: 10.1371/journal.pone.0169177] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 12/13/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Taxillus chinensis (DC.) Danser, the official species of parasitic loranthus that grows by parasitizing other plants, is used in various traditional Chinese medicine prescriptions. ABA-dependent and ABA-independent pathways are two major pathways in response to drought stress for plants and some genes have been reported to play a key role during the dehydration including dehydration-responsive protein RD22, late embryogenesis abundant (LEA) proteins, and various transcription factors (TFs) like MYB and WRKY. However, genes responding to dehydration are still unknown in loranthus. METHODS AND RESULTS Initially, loranthus seeds were characterized as recalcitrant seeds. Then, biological replicates of fresh loranthus seeds (CK), and seeds after being dehydrated for 16 hours (Tac-16) and 36 hours (Tac-36) were sequenced by RNA-Seq, generating 386,542,846 high quality reads. A total of 164,546 transcripts corresponding to 114,971 genes were assembled by Trinity and annotated by mapping them to NCBI non-redundant (NR), UniProt, GO, KEGG pathway and COG databases. Transcriptome profiling identified 60,695, 56,027 and 66,389 transcripts (>1 FPKM) in CK, Tac-16 and Tac-36, respectively. Compared to CK, we obtained 2,102 up-regulated and 1,344 down-regulated transcripts in Tac-16 and 1,649 up-regulated and 2,135 down-regulated transcripts in Tac-36 by using edgeR. Among them some have been reported to function in dehydration process, such as RD22, heat shock proteins (HSP) and various TFs (MYB, WRKY and ethylene-responsive transcription factors). Interestingly, transcripts encoding ribosomal proteins peaked in Tac-16. It is indicated that HSPs and ribosomal proteins may function in early response to drought stress. Raw sequencing data can be accessed in NCBI SRA platform under the accession number SRA309567. CONCLUSIONS This is the first time to profile transcriptome globally in loranthus seeds. Our findings provide insights into the gene regulations of loranthus seeds in response to water loss and expand our current understanding of drought tolerance and germination of seeds.
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Affiliation(s)
- Shugen Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- * E-mail: (XM); (JF)
| | - Limei Pan
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
| | - Jianhua Miao
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
| | - Jine Fu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
- * E-mail: (XM); (JF)
| | - Longhua Bai
- Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Jinghong, China
| | - Zhonglian Zhang
- Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Jinghong, China
| | - Yanhong Guan
- Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Jinghong, China
| | - Changming Mo
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
| | - Hao Huang
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
| | - Maoshan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia
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Michalko J, Renner T, Mészáros P, Socha P, Moravčíková J, Blehová A, Libantová J, Polóniová Z, Matušíková I. Molecular characterization and evolution of carnivorous sundew (Drosera rotundifolia L.) class V β-1,3-glucanase. PLANTA 2017; 245:77-91. [PMID: 27580619 DOI: 10.1007/s00425-016-2592-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/25/2016] [Indexed: 06/06/2023]
Abstract
MAIN CONCLUSION A gene for β-1,3-glucanase was isolated from carnivorous sundew. It is active in leaves and roots, but not in digestive glands. Analyses in transgenic tobacco suggest its function in germination. Ancestral plant β-1,3-glucanases (EC 3.2.1.39) played a role in cell division and cell wall remodelling, but divergent evolution has extended their roles in plant defense against stresses to decomposition of prey in carnivorous plants. As available gene sequences from carnivorous plants are rare, we isolated a glucanase gene from roundleaf sundew (Drosera rotundifolia L.) by a genome walking approach. Computational predictions recognized typical gene features and protein motifs described for other plant β-1,3-glucanases. Phylogenetic reconstructions suggest strong support for evolutionary relatedness to class V β-1,3-glucanases, including homologs that are active in the traps of related carnivorous species. The gene is expressed in sundew vegetative tissues but not in flowers and digestive glands, and encodes for a functional enzyme when expressed in transgenic tobacco. Detailed analyses of the supposed promoter both in silico and in transgenic tobacco suggest that this glucanase plays a role in development. Specific spatiotemporal activity was observed during transgenic seed germination. Later during growth, the sundew promoter was active in marginal and sub-marginal areas of apical true leaf meristems of young tobacco plants. These results suggest that the isolated glucanase gene is regulated endogenously, possibly by auxin. This is the first report on a nuclear gene study from sundew.
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Affiliation(s)
- Jaroslav Michalko
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic
| | - Tanya Renner
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA
| | - Patrik Mészáros
- Department of Botany and Genetics, Faculty of Natural Sciences, Constantine the Philosopher University, Nábrežie mládeže 91, 949 74, Nitra, Slovak Republic
| | - Peter Socha
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic
| | - Jana Moravčíková
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic
| | - Alžbeta Blehová
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University, Mlynská dolina B2, 842 15, Bratislava, Slovak Republic
| | - Jana Libantová
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic
| | - Zuzana Polóniová
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic
| | - Ildikó Matušíková
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic.
- Department of Ecochemistry and Radioecology, University of SS. Cyril and Methodius, J. Herdu 2, 917 01, Trnava, Slovak Republic.
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Li Z, Xu J, Gao Y, Wang C, Guo G, Luo Y, Huang Y, Hu W, Sheteiwy MS, Guan Y, Hu J. The Synergistic Priming Effect of Exogenous Salicylic Acid and H 2O 2 on Chilling Tolerance Enhancement during Maize ( Zea mays L.) Seed Germination. FRONTIERS IN PLANT SCIENCE 2017; 8:1153. [PMID: 28725229 PMCID: PMC5496956 DOI: 10.3389/fpls.2017.01153] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 06/15/2017] [Indexed: 05/18/2023]
Abstract
Chilling stress is an important constraint for maize seedling establishment in the field. To examine the role of salicylic acid (SA) and hydrogen peroxide (H2O2) in response to chilling stress, we investigated the effects of seed priming with SA, H2O2, and SA+H2O2 combination on maize resistance under chilling stress (13°C). Priming with SA, H2O2, and especially SA+H2O2 shortened seed germination time and enhanced seed vigor and seedling growth as compared with hydropriming and non-priming treatments under low temperature. Meanwhile, SA+H2O2 priming notably increased the endogenous H2O2 and SA content, antioxidant enzymes activities and their corresponding genes ZmPAL, ZmSOD4, ZmAPX2, ZmCAT2, and ZmGR expression levels. The α-amylase activity was enhanced to mobilize starch to supply metabolites such as soluble sugar and energy for seed germination under chilling stress. In addition, the SA+H2O2 combination positively up-regulated expressions of gibberellic acid (GA) biosynthesis genes ZmGA20ox1 and ZmGA3ox2, and down-regulated GA catabolism gene ZmGA2ox1 expression; while it promoted GA signaling transduction genes expressions of ZmGID1 and ZmGID2 and decreased the level of seed germination inhibitor gene ZmRGL2. The abscisic acid (ABA) catabolism gene ZmCYP707A2 and the expressions of ZmCPK11 and ZmSnRK2.1 encoding response receptors in ABA signaling pathway were all up-regulated. These results strongly suggested that priming with SA and H2O2 synergistically promoted hormones metabolism and signal transduction, and enhanced energy supply and antioxidant enzymes activities under chilling stress, which were closely relevant with chilling injury alleviation and chilling-tolerance improvement in maize seed. Highlights:Seed germination and seedling growth were significantly improved under chilling stress by priming with SA+H2O2 combination, which was closely relevant with the change of reactive oxygen species, metabolites and energy supply, hormones metabolism and regulation.
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Affiliation(s)
- Zhan Li
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Jungui Xu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Yue Gao
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Chun Wang
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Genyuan Guo
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Ying Luo
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Yutao Huang
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Weimin Hu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Mohamed S. Sheteiwy
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
- Department of Agronomy, Faculty of Agriculture, Mansoura UniversityMansoura, Egypt
| | - Yajing Guan
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
- *Correspondence: Yajing Guan,
| | - Jin Hu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
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94
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Piskurewicz U, Iwasaki M, Susaki D, Megies C, Kinoshita T, Lopez-Molina L. Dormancy-specific imprinting underlies maternal inheritance of seed dormancy in Arabidopsis thaliana. eLife 2016; 5. [PMID: 28005006 PMCID: PMC5243116 DOI: 10.7554/elife.19573] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/21/2016] [Indexed: 01/31/2023] Open
Abstract
Mature seed dormancy is a vital plant trait that prevents germination out of season. In Arabidopsis, the trait can be maternally regulated but the underlying mechanisms sustaining this regulation, its general occurrence and its biological significance among accessions are poorly understood. Upon seed imbibition, the endosperm is essential to repress the germination of dormant seeds. Investigation of genomic imprinting in the mature seed endosperm led us to identify a novel set of imprinted genes that are expressed upon seed imbibition. Remarkably, programs of imprinted gene expression are adapted according to the dormancy status of the seed. We provide direct evidence that imprinted genes play a role in regulating germination processes and that preferential maternal allelic expression can implement maternal inheritance of seed dormancy levels. DOI:http://dx.doi.org/10.7554/eLife.19573.001
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Affiliation(s)
- Urszula Piskurewicz
- Department of Plant Biology, University of Geneva, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Mayumi Iwasaki
- Department of Plant Biology, University of Geneva, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Daichi Susaki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Christian Megies
- Department of Plant Biology, University of Geneva, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Tetsu Kinoshita
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Luis Lopez-Molina
- Department of Plant Biology, University of Geneva, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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95
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Chrobok D, Law SR, Brouwer B, Lindén P, Ziolkowska A, Liebsch D, Narsai R, Szal B, Moritz T, Rouhier N, Whelan J, Gardeström P, Keech O. Dissecting the Metabolic Role of Mitochondria during Developmental Leaf Senescence. PLANT PHYSIOLOGY 2016; 172:2132-2153. [PMID: 27744300 PMCID: PMC5129728 DOI: 10.1104/pp.16.01463] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/13/2016] [Indexed: 05/20/2023]
Abstract
The functions of mitochondria during leaf senescence, a type of programmed cell death aimed at the massive retrieval of nutrients from the senescing organ to the rest of the plant, remain elusive. Here, combining experimental and analytical approaches, we showed that mitochondrial integrity in Arabidopsis (Arabidopsis thaliana) is conserved until the latest stages of leaf senescence, while their number drops by 30%. Adenylate phosphorylation state assays and mitochondrial respiratory measurements indicated that the leaf energy status also is maintained during this time period. Furthermore, after establishing a curated list of genes coding for products targeted to mitochondria, we analyzed in isolation their transcript profiles, focusing on several key mitochondrial functions, such as the tricarboxylic acid cycle, mitochondrial electron transfer chain, iron-sulfur cluster biosynthesis, transporters, as well as catabolic pathways. In tandem with a metabolomic approach, our data indicated that mitochondrial metabolism was reorganized to support the selective catabolism of both amino acids and fatty acids. Such adjustments would ensure the replenishment of α-ketoglutarate and glutamate, which provide the carbon backbones for nitrogen remobilization. Glutamate, being the substrate of the strongly up-regulated cytosolic glutamine synthase, is likely to become a metabolically limiting factor in the latest stages of developmental leaf senescence. Finally, an evolutionary age analysis revealed that, while branched-chain amino acid and proline catabolism are very old mitochondrial functions particularly enriched at the latest stages of leaf senescence, auxin metabolism appears to be rather newly acquired. In summation, our work shows that, during developmental leaf senescence, mitochondria orchestrate catabolic processes by becoming increasingly central energy and metabolic hubs.
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Affiliation(s)
- Daria Chrobok
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Simon R Law
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Bastiaan Brouwer
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Pernilla Lindén
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Agnieszka Ziolkowska
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Daniela Liebsch
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Reena Narsai
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Bozena Szal
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Thomas Moritz
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Nicolas Rouhier
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - James Whelan
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Per Gardeström
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.);
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.);
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.);
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
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96
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Wang Z, Chen F, Li X, Cao H, Ding M, Zhang C, Zuo J, Xu C, Xu J, Deng X, Xiang Y, Soppe WJJ, Liu Y. Arabidopsis seed germination speed is controlled by SNL histone deacetylase-binding factor-mediated regulation of AUX1. Nat Commun 2016; 7:13412. [PMID: 27834370 PMCID: PMC5114640 DOI: 10.1038/ncomms13412] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 09/30/2016] [Indexed: 12/22/2022] Open
Abstract
Histone acetylation is known to affect the speed of seed germination, but the molecular regulatory basis of this remains ambiguous. Here we report that loss of function of two histone deacetylase-binding factors, SWI-INDEPENDENT3 (SIN3)-LIKE1 (SNL1) and SNL2, results in accelerated radicle protrusion and growth during seed germination. AUXIN RESISTANT 1 (AUX1) is identified as a key factor in this process, enhancing germination speed downstream of SNL1 and SNL2. AUX1 expression and histone H3 acetylation at lysines 9 and 18 is regulated by SNL1 and SNL2. The D-type cyclins encoding genes CYCD1;1 and CYCD4;1 display increased expression in AUX1 over-expression lines and the snl1snl2 double mutant. Accordingly, knockout of CYCD4;1 reduces seed germination speed of AUX1 over-expression lines and snl1snl2 suggesting the importance of cell cycling for radicle protrusion during seed germination. Together, our work identifies AUX1 as a link between histone acetylation mediated by SNL1 and SNL2, and radicle growth promoted by CYCD1;1 and CYCD4;1 during seed germination. Histone acetylation influences the speed of seed germination. Here, Wang et al. show that loss of the SNL1/SNL2 histone deacetylase binding factors accelerates seed germination and provide evidence that they act by regulating the expression of AUX1 which in turn influences cell division.
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Affiliation(s)
- Zhi Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaoying Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Meng Ding
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cun Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaonan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jimei Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Deng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yong Xiang
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Wim J J Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, 53115 Bonn, Germany
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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97
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Liberatore KL, Dukowic-Schulze S, Miller ME, Chen C, Kianian SF. The role of mitochondria in plant development and stress tolerance. Free Radic Biol Med 2016; 100:238-256. [PMID: 27036362 DOI: 10.1016/j.freeradbiomed.2016.03.033] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/25/2016] [Accepted: 03/28/2016] [Indexed: 01/03/2023]
Abstract
Eukaryotic cells require orchestrated communication between nuclear and organellar genomes, perturbations in which are linked to stress response and disease in both animals and plants. In addition to mitochondria, which are found across eukaryotes, plant cells contain a second organelle, the plastid. Signaling both among the organelles (cytoplasmic) and between the cytoplasm and the nucleus (i.e. nuclear-cytoplasmic interactions (NCI)) is essential for proper cellular function. A deeper understanding of NCI and its impact on development, stress response, and long-term health is needed in both animal and plant systems. Here we focus on the role of plant mitochondria in development and stress response. We compare and contrast features of plant and animal mitochondrial genomes (mtDNA), particularly highlighting the large and highly dynamic nature of plant mtDNA. Plant-based tools are powerful, yet underutilized, resources for enhancing our fundamental understanding of NCI. These tools also have great potential for improving crop production. Across taxa, mitochondria are most abundant in cells that have high energy or nutrient demands as well as at key developmental time points. Although plant mitochondria act as integrators of signals involved in both development and stress response pathways, little is known about plant mtDNA diversity and its impact on these processes. In humans, there are strong correlations between particular mitotypes (and mtDNA mutations) and developmental differences (or disease). We propose that future work in plants should focus on defining mitotypes more carefully and investigating their functional implications as well as improving techniques to facilitate this research.
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Affiliation(s)
- Katie L Liberatore
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States.
| | | | - Marisa E Miller
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, United States
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, United States
| | - Shahryar F Kianian
- United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, United States; Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States
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98
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The Arabidopsis MIEL1 E3 ligase negatively regulates ABA signalling by promoting protein turnover of MYB96. Nat Commun 2016; 7:12525. [PMID: 27615387 PMCID: PMC5027273 DOI: 10.1038/ncomms12525] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/07/2016] [Indexed: 01/31/2023] Open
Abstract
The phytohormone abscisic acid (ABA) regulates plant responses to various environmental challenges. Controlled protein turnover is an important component of ABA signalling. Here we show that the RING-type E3 ligase MYB30-INTERACTING E3 LIGASE 1 (MIEL1) regulates ABA sensitivity by promoting MYB96 turnover in Arabidopsis. Germination of MIEL1-deficient mutant seeds is hypersensitive to ABA, whereas MIEL1-overexpressing transgenic seeds are less sensitive. MIEL1 can interact with MYB96, a regulator of ABA signalling, and stimulate its ubiquitination and degradation. Genetic analysis shows that MYB96 is epistatic to MIEL1 in the control of ABA sensitivity in seeds. While MIEL1 acts primarily via MYB96 in seed germination, MIEL1 regulates protein turnover of both MYB96 and MYB30 in vegetative tissues. We find that ABA regulates the expression of MYB30-responsive genes during pathogen infection and this regulation is partly dependent on MIEL1. These results suggest that MIEL1 may facilitate crosstalk between ABA and biotic stress signalling. The phytohormone abscisic acid controls plant responses to environmental stress, partly by regulating protein turnover. Here the authors propose that abscisic acid regulates seed germination by promoting degradation of the MYB96 transcription factor via the MIEL1 E3 ubiquitin (Ub) ligase.
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99
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Dekkers BJW, Pearce SP, van Bolderen-Veldkamp RPM, Holdsworth MJ, Bentsink L. Dormant and after-Ripened Arabidopsis thaliana Seeds are Distinguished by Early Transcriptional Differences in the Imbibed State. FRONTIERS IN PLANT SCIENCE 2016; 7:1323. [PMID: 27625677 PMCID: PMC5003841 DOI: 10.3389/fpls.2016.01323] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/18/2016] [Indexed: 05/22/2023]
Abstract
Seed dormancy is a genetically controlled block preventing the germination of imbibed seeds in favorable conditions. It requires a period of dry storage (after-ripening) or certain environmental conditions to be overcome. Dormancy is an important seed trait, which is under selective pressure, to control the seasonal timing of seed germination. Dormant and non-dormant (after-ripened) seeds are characterized by large sets of differentially expressed genes. However, little information is available concerning the temporal and spatial transcriptional changes during early stages of rehydration in dormant and non-dormant seeds. We employed genome-wide transcriptome analysis on seeds of the model plant Arabidopsis thaliana to investigate transcriptional changes in dry seeds upon rehydration. We analyzed gene expression of dormant and after-ripened seeds of the Cvi accession over four time points and two seed compartments (the embryo and surrounding single cell layer endosperm), during the first 24 h after sowing. This work provides a global view of gene expression changes in dormant and non-dormant seeds with temporal and spatial detail, and these may be visualized via a web accessible tool (http://www.wageningenseedlab.nl/resources). A large proportion of transcripts change similarly in both dormant and non-dormant seeds upon rehydration, however, the first differences in transcript abundances become visible shortly after the initiation of imbibition, indicating that changes induced by after-ripening are detected and responded to rapidly upon rehydration. We identified several gene expression profiles which contribute to differential gene expression between dormant and non-dormant samples. Genes with enhanced expression in the endosperm of dormant seeds were overrepresented for stress-related Gene Ontology categories, suggesting a protective role for the endosperm against biotic and abiotic stress to support persistence of the dormant seed in its environment.
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Affiliation(s)
- Bas J. W. Dekkers
- Department of Molecular Plant Physiology, Utrecht UniversityUtrecht, Netherlands
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Simon P. Pearce
- Faculty of Biology, Medicine and Health, University of ManchesterManchester, UK
- School of Mathematics, University of ManchesterManchester, UK
| | - R. P. M. van Bolderen-Veldkamp
- Department of Molecular Plant Physiology, Utrecht UniversityUtrecht, Netherlands
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Michael J. Holdsworth
- Division of Plant and Crop Science, School of Biosciences, University of NottinghamLeicestershire, UK
| | - Leónie Bentsink
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
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100
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Vesty EF, Saidi Y, Moody LA, Holloway D, Whitbread A, Needs S, Choudhary A, Burns B, McLeod D, Bradshaw SJ, Bae H, King BC, Bassel GW, Simonsen HT, Coates JC. The decision to germinate is regulated by divergent molecular networks in spores and seeds. THE NEW PHYTOLOGIST 2016; 211:952-66. [PMID: 27257104 PMCID: PMC4950004 DOI: 10.1111/nph.14018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/16/2016] [Indexed: 05/15/2023]
Abstract
Dispersal is a key step in land plant life cycles, usually via formation of spores or seeds. Regulation of spore- or seed-germination allows control over the timing of transition from one generation to the next, enabling plant dispersal. A combination of environmental and genetic factors determines when seed germination occurs. Endogenous hormones mediate this decision in response to the environment. Less is known about how spore germination is controlled in earlier-evolving nonseed plants. Here, we present an in-depth analysis of the environmental and hormonal regulation of spore germination in the model bryophyte Physcomitrella patens (Aphanoregma patens). Our data suggest that the environmental signals regulating germination are conserved, but also that downstream hormone integration pathways mediating these responses in seeds were acquired after the evolution of the bryophyte lineage. Moreover, the role of abscisic acid and diterpenes (gibberellins) in germination assumed much greater importance as land plant evolution progressed. We conclude that the endogenous hormone signalling networks mediating germination in response to the environment may have evolved independently in spores and seeds. This paves the way for future research about how the mechanisms of plant dispersal on land evolved.
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Affiliation(s)
- Eleanor F. Vesty
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Younousse Saidi
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Laura A. Moody
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Daniel Holloway
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Amy Whitbread
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Sarah Needs
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Anushree Choudhary
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Bethany Burns
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Daniel McLeod
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Susan J. Bradshaw
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Hansol Bae
- Department of Systems BiologyTechnical University of DenmarkSøltofts Plads, 2800 KgsLyngbyDenmark
| | - Brian Christopher King
- Department of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
| | - George W. Bassel
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Henrik Toft Simonsen
- Department of Systems BiologyTechnical University of DenmarkSøltofts Plads, 2800 KgsLyngbyDenmark
| | - Juliet C. Coates
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
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