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Liu Z, Gui J, Yan Y, Zhang H, He J. Transcriptomic Analysis of the Dehydration Rate of Mature Rice ( Oryza sativa) Seeds. Int J Mol Sci 2023; 24:11527. [PMID: 37511287 PMCID: PMC10380403 DOI: 10.3390/ijms241411527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/30/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
In this study, a transcriptomic analysis of the dehydration rate of mature rice seeds was conducted to explore candidate genes related to the dehydration rate and provide a theoretical basis for breeding and utilization. We selected two rice cultivars for testing (Baghlani Nangarhar, an extremely rapid dehydration genotype, and Saturn, a slow dehydration genotype) based on the results determined by previous studies conducted on the screening of 165 germplasm materials for dehydration rate phenotypes. A rapid dehydration experiment performed on these two types of seeds was conducted. Four comparative groups were set up under control and dehydration conditions. The differentially expressed genes (DEGs) were quantified via transcriptome sequencing and real-time quantitative PCR (RT-qPCR). GO (Gene ontology) and KEGG(Kyoto Encyclopedia of Genes and Genomes) analyses were also conducted. In Baghlani Nangarhar, 53 DEGs were screened, of which 33 were up-regulated and 20 were down-regulated. In Saturn, 25 DEGs were screened, of which 19 were up-regulated and 6 were down-regulated. The results of the GO analysis show that the sites of action of the differentially expressed genes enriched in the rapid dehydration modes are concentrated in the cytoplasm, internal components of the membrane, and nucleosomes. They play regulatory roles in the processes of catalysis, binding, translocation, transcription, protein folding, degradation, and replication. They are also involved in adaptive responses to adverse external environments, such as reactive oxygen species and high temperature. The KEGG analysis showed that protein processing in the endoplasmic reticulum, amino acid biosynthesis, and oxidative phosphorylation were the main metabolic pathways that were enriched. The key differentially expressed genes and the most important metabolic pathways identified in the rapidly and slowly dehydrated genotypes were protein processing in the endoplasmic reticulum and oxidative phosphorylation metabolism. They were presumed to have important regulatory roles in the mechanisms of stress/defense, energy metabolism, protein synthesis/folding, and signal transduction during the dehydration and drying of mature seeds. The results of this study can potentially provide valuable information for further research on the genes and metabolic pathways related to the dehydration rate of mature rice seeds, and provide theoretical guidance for the selection and breeding of new rice germplasm that can be rapidly dehydrated at the mature stage.
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Affiliation(s)
- Zhongqi Liu
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Jinxin Gui
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Yuntao Yan
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Haiqing Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Jiwai He
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
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2
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Laloum T, Carvalho SD, Martín G, Richardson DN, Cruz TMD, Carvalho RF, Stecca KL, Kinney AJ, Zeidler M, Barbosa ICR, Duque P. The SCL30a SR protein regulates ABA-dependent seed traits and germination under stress. PLANT, CELL & ENVIRONMENT 2023; 46:2112-2127. [PMID: 37098235 DOI: 10.1111/pce.14593] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 05/23/2023]
Abstract
SR proteins are conserved RNA-binding proteins best known as splicing regulators that have also been implicated in other steps of gene expression. Despite mounting evidence for a role in plant development and stress responses, the molecular pathways underlying SR protein regulation of these processes remain poorly understood. Here we show that the plant-specific SCL30a SR protein negatively regulates ABA signaling to control seed traits and stress responses during germination in Arabidopsis. Transcriptome-wide analyses revealed that loss of SCL30a function barely affects splicing, but largely induces ABA-responsive gene expression and genes repressed during germination. Accordingly, scl30a mutant seeds display delayed germination and hypersensitivity to ABA and high salinity, while transgenic plants overexpressing SCL30a exhibit reduced ABA and salt stress sensitivity. An ABA biosynthesis inhibitor rescues the enhanced mutant seed stress sensitivity, and epistatic analyses confirm that this hypersensitivity requires a functional ABA pathway. Finally, seed ABA levels are unchanged by altered SCL30a expression, indicating that the gene promotes seed germination under stress by reducing sensitivity to the phytohormone. Our results reveal a new player in ABA-mediated control of early development and stress response.
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Affiliation(s)
- Tom Laloum
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | | | | | | | | - Kevin L Stecca
- Crop Genetics Research and Development, DuPont Experimental Station, Wilmington, Delaware, USA
| | - Anthony J Kinney
- Crop Genetics Research and Development, DuPont Experimental Station, Wilmington, Delaware, USA
| | - Mathias Zeidler
- Institute of Plant Physiology, Justus-Liebig-University Gießen, Gießen, Germany
| | | | - Paula Duque
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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3
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Bai B, Schiffthaler B, van der Horst S, Willems L, Vergara A, Karlström J, Mähler N, Delhomme N, Bentsink L, Hanson J. SeedTransNet: a directional translational network revealing regulatory patterns during seed maturation and germination. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2416-2432. [PMID: 36208446 PMCID: PMC10082931 DOI: 10.1093/jxb/erac394] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/06/2022] [Indexed: 06/06/2023]
Abstract
Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.
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Affiliation(s)
- Bing Bai
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Bastian Schiffthaler
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Sjors van der Horst
- Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Leo Willems
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Alexander Vergara
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jacob Karlström
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Niklas Mähler
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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4
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Mechanism of [CO 2] Enrichment Alleviated Drought Stress in the Roots of Cucumber Seedlings Revealed via Proteomic and Biochemical Analysis. Int J Mol Sci 2022; 23:ijms232314911. [PMID: 36499239 PMCID: PMC9737773 DOI: 10.3390/ijms232314911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Cucumber is one of the most widely cultivated greenhouse vegetables, and its quality and yield are threatened by drought stress. Studies have shown that carbon dioxide concentration ([CO2]) enrichment can alleviate drought stress in cucumber seedlings; however the mechanism of this [CO2] enrichment effect on root drought stress is not clear. In this study, the effects of different drought stresses (simulated with 0, 5% and 10% PEG 6000, i.e., no, moderate, and severe drought stress) and [CO2] (400 μmol·mol-1 and 800 ± 40 μmol·mol-1) on the cucumber seedling root proteome were analyzed using the tandem mass tag (TMT) quantitative proteomics method. The results showed that after [CO2] enrichment, 346 differentially accumulating proteins (DAPs) were found only under moderate drought stress, 27 DAPs only under severe drought stress, and 34 DAPs under both moderate and severe drought stress. [CO2] enrichment promoted energy metabolism, amino acid metabolism, and secondary metabolism, induced the expression of proteins related to root cell wall and cytoskeleton metabolism, effectively maintained the balance of protein processing and degradation, and enhanced the cell wall regulation ability. However, the extent to which [CO2] enrichment alleviated drought stress in cucumber seedling roots was limited under severe drought stress, which may be due to excessive damage to the seedlings.
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Sano N, Malabarba J, Chen Z, Gaillard S, Windels D, Verdier J. Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:1059493. [PMID: 36507374 PMCID: PMC9729785 DOI: 10.3389/fpls.2022.1059493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Desiccation tolerance (DT) has contributed greatly to the adaptation of land plants to severe water-deficient conditions. DT is mostly observed in reproductive parts in flowering plants such as seeds. The seed DT is lost at early post germination stage but is temporally re-inducible in 1 mm radicles during the so-called DT window following a PEG treatment before being permanently silenced in 5 mm radicles of germinating seeds. The molecular mechanisms that activate/reactivate/silence DT in developing and germinating seeds have not yet been elucidated. Here, we analyzed chromatin dynamics related to re-inducibility of DT before and after the DT window at early germination in Medicago truncatula radicles to determine if DT-associated genes were transcriptionally regulated at the chromatin levels. Comparative transcriptome analysis of these radicles identified 948 genes as DT re-induction-related genes, positively correlated with DT re-induction. ATAC-Seq analyses revealed that the chromatin state of genomic regions containing these genes was clearly modulated by PEG treatment and affected by growth stages with opened chromatin in 1 mm radicles with PEG (R1P); intermediate openness in 1 mm radicles without PEG (R1); and condensed chromatin in 5 mm radicles without PEG (R5). In contrast, we also showed that the 103 genes negatively correlated with the re-induction of DT did not show any transcriptional regulation at the chromatin level. Additionally, ChIP-Seq analyses for repressive marks H2AK119ub and H3K27me3 detected a prominent signal of H3K27me3 on the DT re-induction-related gene sequences at R5 but not in R1 and R1P. Moreover, no clear H2AK119ub marks was observed on the DT re-induction-related gene sequences at both developmental radicle stages, suggesting that silencing of DT process after germination will be mainly due to H3K27me3 marks by the action of the PRC2 complex, without involvement of PRC1 complex. The dynamic of chromatin changes associated with H3K27me3 were also confirmed on seed-specific genes encoding potential DT-related proteins such as LEAs, oleosins and transcriptional factors. However, several transcriptional factors did not show a clear link between their decrease of chromatin openness and H3K27me3 levels, suggesting that their accessibility may also be regulated by additional factors, such as other histone modifications. Finally, in order to make these comprehensive genome-wide analyses of transcript and chromatin dynamics useful to the scientific community working on early germination and DT, we generated a dedicated genome browser containing all these data and publicly available at https://iris.angers.inrae.fr/mtseedepiatlas/jbrowse/?data=Mtruncatula.
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Abdullah-Zawawi MR, Govender N, Harun S, Muhammad NAN, Zainal Z, Mohamed-Hussein ZA. Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom. PLANTS (BASEL, SWITZERLAND) 2022; 11:2614. [PMID: 36235479 PMCID: PMC9573505 DOI: 10.3390/plants11192614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/05/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performance computing and development of computational tools for biological sciences have assisted in silico functional prediction of unknown genes, proteins and metabolites, otherwise known as uncharacterized. The systems biology approach includes data collection and filtration, system modelling, experimentation and the establishment of new hypotheses for experimental validation. Informatics technologies add meaningful sense to the output generated by complex bioinformatics algorithms, which are now freely available in a user-friendly graphical user interface. These resources accentuate gene function prediction at a relatively minimal cost and effort. Herein, we present a comprehensive view of relevant approaches available for system-level gene function prediction in the plant kingdom. Together, the most recent applications and sought-after principles for gene mining are discussed to benefit the plant research community. A realistic tabulation of plant genomic resources is included for a less laborious and accurate candidate gene discovery in basic plant research and improvement strategies.
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Affiliation(s)
- Muhammad-Redha Abdullah-Zawawi
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Nisha Govender
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Sarahani Harun
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Zamri Zainal
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
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Pagano A, Zannino L, Pagano P, Doria E, Dondi D, Macovei A, Biggiogera M, Araújo SDS, Balestrazzi A. Changes in genotoxic stress response, ribogenesis and PAP (3'-phosphoadenosine 5'-phosphate) levels are associated with loss of desiccation tolerance in overprimed Medicago truncatula seeds. PLANT, CELL & ENVIRONMENT 2022; 45:1457-1473. [PMID: 35188276 PMCID: PMC9311706 DOI: 10.1111/pce.14295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 05/06/2023]
Abstract
Re-establishment of desiccation tolerance is essential for the survival of germinated seeds facing water deficit in the soil. The molecular and ultrastructural features of desiccation tolerance maintenance and loss within the nuclear compartment are not fully resolved. In the present study, the impact of desiccation-induced genotoxic stress on nucleolar ultrastructure and ribogenesis was explored along the rehydration-dehydration cycle applied in standard seed vigorization protocols. Primed and overprimed Medicago truncatula seeds, obtained through hydropriming followed by desiccation (dry-back), were analysed. In contrast to desiccation-tolerant primed seeds, overprimed seeds enter irreversible germination and do not survive dry-back. Reactive oxygen species, DNA damage and expression profiles of antioxidant/DNA Damage Response genes were measured, as main hallmarks of the seed response to desiccation stress. Nuclear ultrastructural features were also investigated. Overprimed seeds subjected to dry-back revealed altered rRNA accumulation profiles and up-regulation of genes involved in ribogenesis control. The signal molecule PAP (3'-phosphoadenosine 5'-phosphate) accumulated during dry-back only in primed seeds, as a distinctive feature of desiccation tolerance. The presented results show the molecular and ultrastructural landscapes of the seed desiccation response, including substantial changes in nuclear organization.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Lorena Zannino
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Paola Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Enrico Doria
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Daniele Dondi
- Department of ChemistryUniversity of PaviaPaviaItaly
| | - Anca Macovei
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Marco Biggiogera
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Susana de Sousa Araújo
- Association BLC3‐Technology and Innovation CampusCentre Bio R&D UnitMacedo de CavaleirosPortugal
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
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Peng L, Huang X, Qi M, Pritchard HW, Xue H. Mechanistic insights derived from re-establishment of desiccation tolerance in germinating xerophytic seeds: Caragana korshinskii as an example. FRONTIERS IN PLANT SCIENCE 2022; 13:1029997. [PMID: 36420023 PMCID: PMC9677110 DOI: 10.3389/fpls.2022.1029997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 09/27/2022] [Indexed: 05/13/2023]
Abstract
Germplasm conservation strongly depends on the desiccation tolerance (DT) of seeds. Xerophytic seeds have strong desiccation resistance, which makes them excellent models to study DT. Although some experimental strategies have been applied previously, most methods are difficult to apply to xerophytic seeds. In this review, we attempted to synthesize current strategies for the study of seed DT and provide an in-depth look at Caragana korshinskii as an example. First, we analyze congenital advantages of xerophytes in the study of seed DT. Second, we summarize several strategies used to study DT and illustrate a suitable strategy for xerophytic species. Then, based on our previous studies work with C. korshinskii, a feasible technical strategy for DT re-establishment is provided and we provide illustrate some special molecular mechanisms seen in xerophytic seeds. Finally, several steps to unveil the DT mechanism of xerophytic seeds are suggested, and three scientific questions that the field should consider are listed. We hope to optimize and utilize this strategy for more xerophytic species to more systematically decipher the physiological and molecular processes of seed DT and provide more candidate genes for molecular breeding.
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Affiliation(s)
- Long Peng
- The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xu Huang
- National Engineering Research Center of Tree breeding and Ecological remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Manyao Qi
- National Engineering Research Center of Tree breeding and Ecological remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hugh W. Pritchard
- Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
- Royal Botanic Gardens, Kew, Wakehurst, West Sussex, United Kingdom
| | - Hua Xue
- National Engineering Research Center of Tree breeding and Ecological remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- *Correspondence: Hua Xue,
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9
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Matilla AJ. The Orthodox Dry Seeds Are Alive: A Clear Example of Desiccation Tolerance. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010020. [PMID: 35009023 PMCID: PMC8747232 DOI: 10.3390/plants11010020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 05/17/2023]
Abstract
To survive in the dry state, orthodox seeds acquire desiccation tolerance. As maturation progresses, the seeds gradually acquire longevity, which is the total timespan during which the dry seeds remain viable. The desiccation-tolerance mechanism(s) allow seeds to remain dry without losing their ability to germinate. This adaptive trait has played a key role in the evolution of land plants. Understanding the mechanisms for seed survival after desiccation is one of the central goals still unsolved. That is, the cellular protection during dry state and cell repair during rewatering involves a not entirely known molecular network(s). Although desiccation tolerance is retained in seeds of higher plants, resurrection plants belonging to different plant lineages keep the ability to survive desiccation in vegetative tissue. Abscisic acid (ABA) is involved in desiccation tolerance through tight control of the synthesis of unstructured late embryogenesis abundant (LEA) proteins, heat shock thermostable proteins (sHSPs), and non-reducing oligosaccharides. During seed maturation, the progressive loss of water induces the formation of a so-called cellular "glass state". This glassy matrix consists of soluble sugars, which immobilize macromolecules offering protection to membranes and proteins. In this way, the secondary structure of proteins in dry viable seeds is very stable and remains preserved. ABA insensitive-3 (ABI3), highly conserved from bryophytes to Angiosperms, is essential for seed maturation and is the only transcription factor (TF) required for the acquisition of desiccation tolerance and its re-induction in germinated seeds. It is noteworthy that chlorophyll breakdown during the last step of seed maturation is controlled by ABI3. This update contains some current results directly related to the physiological, genetic, and molecular mechanisms involved in survival to desiccation in orthodox seeds. In other words, the mechanisms that facilitate that an orthodox dry seed is a living entity.
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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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Maula T, Vahvelainen N, Tossavainen H, Koivunen T, T. Pöllänen M, Johansson A, Permi P, Ihalin R. Decreased temperature increases the expression of a disordered bacterial late embryogenesis abundant (LEA) protein that enhances natural transformation. Virulence 2021; 12:1239-1257. [PMID: 33939577 PMCID: PMC8096337 DOI: 10.1080/21505594.2021.1918497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/22/2021] [Accepted: 04/03/2021] [Indexed: 11/02/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins are important players in the management of responses to stressful conditions, such as drought, high salinity, and changes in temperature. Many LEA proteins do not have defined three-dimensional structures, so they are intrinsically disordered proteins (IDPs) and are often highly hydrophilic. Although LEA-like sequences have been identified in bacterial genomes, the functions of bacterial LEA proteins have been studied only recently. Sequence analysis of outer membrane interleukin receptor I (BilRI) from the oral pathogen Aggregatibacter actinomycetemcomitans indicated that it shared sequence similarity with group 3/3b/4 LEA proteins. Comprehensive nuclearcgq magnetic resonance (NMR) studies confirmed its IDP nature, and expression studies in A. actinomycetemcomitans harboring a red fluorescence reporter protein-encoding gene revealed that bilRI promoter expression was increased at decreased temperatures. The amino acid backbone of BilRI did not stimulate either the production of reactive oxygen species from human leukocytes or the production of interleukin-6 from human macrophages. Moreover, BilRI-specific IgG antibodies could not be detected in the sera of A. actinomycetemcomitans culture-positive periodontitis patients. Since the bilRI gene is located near genes involved in natural competence (i.e., genes associated with the uptake of extracellular (eDNA) and its incorporation into the genome), we also investigated the role of BilRI in these events. Compared to wild-type cells, the ΔbilRI mutants showed a lower transformation efficiency, which indicates either a direct or indirect role in natural competence. In conclusion, A. actinomycetemcomitans might express BilRI, especially outside the host, to survive under stressful conditions and improve its transmission potential.
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Affiliation(s)
- Terhi Maula
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Nelli Vahvelainen
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Helena Tossavainen
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Tuuli Koivunen
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Anders Johansson
- Division of Molecular Periodontology, Department of Odontology, Umeå University, Umeå, Sweden
| | - Perttu Permi
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Riikka Ihalin
- Department of Life Technologies, University of Turku, Turku, Finland
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Ambastha V, Matityahu I, Tidhar D, Leshem Y. RabA2b Overexpression Alters the Plasma-Membrane Proteome and Improves Drought Tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:738694. [PMID: 34691115 PMCID: PMC8526897 DOI: 10.3389/fpls.2021.738694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/13/2021] [Indexed: 06/07/2023]
Abstract
Rab proteins are small GTPases that are important in the regulation of vesicle trafficking. Through data mining, we identified RabA2b to be stress responsive, though little is known about the involvement of RabA in plant responses to abiotic stresses. Analysis of the RabA2b native promoter showed strong activity during osmotic stress, which required the stress hormone Abscisic acid (ABA) and was restricted to the vasculature. Sequence analysis of the promoter region identified predicted binding motifs for several ABA-responsive transcription factors. We cloned RabA2b and overexpressed it in Arabidopsis. The resulting transgenic plants were strikingly drought resistant. The reduced water loss observed in detached leaves of the transgenic plants could not be explained by stomatal aperture or density, which was similar in all the genotypes. Subcellular localization studies detected strong colocalization between RabA2b and the plasma membrane (PM) marker PIP2. Further studies of the PM showed, for the first time, a distinguished alteration in the PM proteome as a result of RabA2b overexpression. Proteomic analysis of isolated PM fractions showed enrichment of stress-coping proteins as well as cell wall/cuticle modifiers in the transgenic lines. Finally, the cuticle permeability of transgenic leaves was significantly reduced compared to the wild type, suggesting that it plays a role in its drought resistant properties. Overall, these data provide new insights into the roles and modes of action of RabA2b during water stresses, and indicate that increased RabA2b mediated PM trafficking can affect the PM proteome and increase drought tolerance.
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Affiliation(s)
- Vivek Ambastha
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
| | - Ifat Matityahu
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
| | - Dafna Tidhar
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai College, Upper Galilee, Israel
| | - Yehoram Leshem
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai College, Upper Galilee, Israel
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Arabidopsis LSH8 Positively Regulates ABA Signaling by Changing the Expression Pattern of ABA-Responsive Proteins. Int J Mol Sci 2021; 22:ijms221910314. [PMID: 34638657 PMCID: PMC8508927 DOI: 10.3390/ijms221910314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/19/2021] [Accepted: 09/23/2021] [Indexed: 01/17/2023] Open
Abstract
Phytohormone ABA regulates the expression of numerous genes to significantly affect seed dormancy, seed germination and early seedling responses to biotic and abiotic stresses. However, the function of many ABA-responsive genes remains largely unknown. In order to improve the ABA-related signaling network, we conducted a large-scale ABA phenotype screening. LSH, an important transcription factor family, extensively participates in seedling development and floral organogenesis in plants, but whether its family genes are involved in the ABA signaling pathway has not been reported. Here we describe a new function of the transcription factor LSH8 in an ABA signaling pathway. In this study, we found that LSH8 was localized in the nucleus, and the expression level of LSH8 was significantly induced by exogenous ABA at the transcription level and protein level. Meanwhile, seed germination and root length measurements revealed that lsh8 mutant lines were ABA insensitive, whereas LSH8 overexpression lines showed an ABA-hypersensitive phenotype. With further TMT labeling quantitative proteomic analysis, we found that under ABA treatment, ABA-responsive proteins (ARPs) in the lsh8 mutant presented different changing patterns with those in wild-type Col4. Additionally, the number of ARPs contained in the lsh8 mutant was 397, six times the number in wild-type Col4. In addition, qPCR analysis found that under ABA treatment, LSH8 positively mediated the expression of downstream ABA-related genes of ABI3, ABI5, RD29B and RAB18. These results indicate that in Arabidopsis, LSH8 is a novel ABA regulator that could specifically change the expression pattern of APRs to positively mediate ABA responses.
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Smolikova G, Strygina K, Krylova E, Leonova T, Frolov A, Khlestkina E, Medvedev S. Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects. PLANTS (BASEL, SWITZERLAND) 2021; 10:1884. [PMID: 34579418 PMCID: PMC8467299 DOI: 10.3390/plants10091884] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/02/2021] [Accepted: 09/08/2021] [Indexed: 01/21/2023]
Abstract
Transition from seed to seedling is one of the critical developmental steps, dramatically affecting plant growth and viability. Before plants enter the vegetative phase of their ontogenesis, massive rearrangements of signaling pathways and switching of gene expression programs are required. This results in suppression of the genes controlling seed maturation and activation of those involved in regulation of vegetative growth. At the level of hormonal regulation, these events are controlled by the balance of abscisic acid and gibberellins, although ethylene, auxins, brassinosteroids, cytokinins, and jasmonates are also involved. The key players include the members of the LAFL network-the transcription factors LEAFY COTYLEDON1 and 2 (LEC 1 and 2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (FUS3), as well as DELAY OF GERMINATION1 (DOG1). They are the negative regulators of seed germination and need to be suppressed before seedling development can be initiated. This repressive signal is mediated by chromatin remodeling complexes-POLYCOMB REPRESSIVE COMPLEX 1 and 2 (PRC1 and PRC2), as well as PICKLE (PKL) and PICKLE-RELATED2 (PKR2) proteins. Finally, epigenetic methylation of cytosine residues in DNA, histone post-translational modifications, and post-transcriptional downregulation of seed maturation genes with miRNA are discussed. Here, we summarize recent updates in the study of hormonal and epigenetic switches involved in regulation of the transition from seed germination to the post-germination stage.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ksenia Strygina
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Ekaterina Krylova
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany; (T.L.); (A.F.)
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany; (T.L.); (A.F.)
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena Khlestkina
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia;
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Bizouerne E, Buitink J, Vu BL, Vu JL, Esteban E, Pasha A, Provart N, Verdier J, Leprince O. Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour. BMC PLANT BIOLOGY 2021; 21:124. [PMID: 33648457 PMCID: PMC7923611 DOI: 10.1186/s12870-021-02889-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/11/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures associated with desiccation tolerance, longevity, germination under water stress and dormancy. RESULTS During maturation, 15,173 differentially expressed genes were detected, forming a gene network representing 21 expression modules, with 3 being specific to seed coat and embryo and 5 to the endosperm. A gene-trait significance measure identified a common gene module between endosperm and embryo associated with desiccation tolerance and conserved with non-endospermic seeds. In addition to genes involved in protection such LEA and HSP and ABA response, the module included antioxidant and repair genes. Dormancy was released concomitantly with the increase in longevity throughout fruit ripening until 14 days after the red fruit stage. This was paralleled by an increase in SlDOG1-2 and PROCERA transcripts. The progressive increase in seed vigour was captured by three gene modules, one in common between embryo and endosperm and two tissue-specific. The common module was enriched with genes associated with mRNA processing in chloroplast and mitochondria (including penta- and tetratricopeptide repeat-containing proteins) and post-transcriptional regulation, as well several flowering genes. The embryo-specific module contained homologues of ABI4 and CHOTTO1 as hub genes associated with seed vigour, whereas the endosperm-specific module revealed a diverse set of processes that were related to genome stability, defence against pathogens and ABA/GA response genes. CONCLUSION The spatio-temporal co-expression atlas of tomato seed maturation will serve as a valuable resource for the in-depth understanding of the dynamics of gene expression associated with the acquisition of seed vigour at the tissue level.
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Affiliation(s)
- Elise Bizouerne
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Julia Buitink
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Benoît Ly Vu
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Joseph Ly Vu
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Eddi Esteban
- Department of Cell and Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jérôme Verdier
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Olivier Leprince
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France.
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Wang Y, Yi N, Hu Y, Zhou X, Jiang H, Lin Q, Chen R, Liu H, Gu Y, Tong C, Lu M, Zhang J, Zhang B, Peng L, Li L. Molecular Signatures and Networks of Cardiomyocyte Differentiation in Humans and Mice. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:696-711. [PMID: 32769060 PMCID: PMC7412763 DOI: 10.1016/j.omtn.2020.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/05/2020] [Accepted: 07/06/2020] [Indexed: 12/23/2022]
Abstract
Cardiomyocyte differentiation derived from embryonic stem cells (ESCs) is a complex process involving molecular regulation of multiple levels. In this study, we first identify and compare differentially expressed gene (DEG) signatures of ESC-derived cardiomyocyte differentiation (ESCDCD) in humans and mice. Then, the multiscale embedded gene co-expression network analysis (MEGENA) of the human ESCDCD dataset is performed to identify 212 significantly co-expressed gene modules, which capture well the regulatory information of cardiomyocyte differentiation. Three modules respectively involved in the regulation of stem cell pluripotency, Wnt, and calcium pathways are enriched in the DEG signatures of the differentiation phase transition in the two species. Three human-specific cardiomyocyte differentiation phase transition modules are identified. Moreover, the potential regulation mechanisms of transcription factors during cardiomyocyte differentiation are also illustrated. Finally, several novel key drivers of ESCDCD are identified with the evidence of their expression during mouse embryonic cardiomyocyte differentiation. Using an integrative network analysis, the core molecular signatures and gene subnetworks (modules) underlying cardiomyocyte lineage commitment are identified in both humans and mice. Our findings provide a global picture of gene-gene co-regulation and identify key regulators during ESCDCD.
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Affiliation(s)
- Yumei Wang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Na Yi
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Yi Hu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Hanyu Jiang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Qin Lin
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Rou Chen
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Huan Liu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Yanqiong Gu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Chang Tong
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Min Lu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Junfang Zhang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Luying Peng
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China.
| | - Li Li
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China.
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16
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Tian R, Wang F, Zheng Q, Niza VMAGE, Downie AB, Perry SE. Direct and indirect targets of the arabidopsis seed transcription factor ABSCISIC ACID INSENSITIVE3. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1679-1694. [PMID: 32445409 DOI: 10.1111/tpj.14854] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 05/09/2020] [Accepted: 05/15/2020] [Indexed: 05/04/2023]
Abstract
Arabidopsis thaliana ABSCISIC ACID INSENSITIVE3 (ABI3) is a transcription factor in the B3 domain family. ABI3, along with B3 domain transcription factors LEAFY COTYLEDON2 (LEC2) and FUSCA3 (FUS3), and LEC1, a subunit of the CCAAT box-binding complex, form the so-called LAFL network to control various aspects of seed development and maturation. ABI3 also contributes to the abscisic acid (ABA) response. We report on chromatin immunoprecipitation-tiling array experiments to map binding sites for ABI3 globally. We also assessed transcriptomes in response to ABI3 by comparing developing abi3-5 and wild-type seeds and combined this information to ascertain direct and indirect responsive ABI3 target genes. ABI3 can induce and repress its transcription of target genes directly and some intriguing differences exist in cis motifs between these groups of genes. Directly regulated targets reflect the role of ABI3 in seed maturation, desiccation tolerance, entry into a quiescent state and longevity. Interestingly, ABI3 directly represses a gene encoding a microRNA (MIR160B) that targets AUXIN RESPONSE FACTOR (ARF)10 and ARF16 that are involved in establishment of dormancy. In addition, ABI3, like FUS3, regulates genes encoding MIR156 but while FUS3 only induces genes encoding this product, ABI3 induces these genes during the early stages of seed development, but represses these genes during late development. The interplay between ABI3, the other LAFL genes, and the VP1/ABI3-LIKE (VAL) genes, which are involved in the transition to seedling development are examined and reveal complex interactions controlling development.
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Affiliation(s)
- Ran Tian
- UK Seed Biology Group, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Fangfang Wang
- UK Seed Biology Group, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Qiaolin Zheng
- UK Seed Biology Group, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Venus M A G E Niza
- UK Seed Biology Group, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - A Bruce Downie
- UK Seed Biology Group, Department of Horticulture, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Sharyn E Perry
- UK Seed Biology Group, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
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17
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Alipour S, Wojciechowska N, Stolarska E, Bilska K, Kalemba EM. NAD(P)-Driven Redox Status Contributes to Desiccation Tolerance in Acer seeds. PLANT & CELL PHYSIOLOGY 2020; 61:1158-1167. [PMID: 32267948 DOI: 10.1093/pcp/pcaa044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Desiccation tolerance is a developmental program enabling seed survival in a dry state and is common in seeds categorized as orthodox. We focused on NAD and its phosphorylated form (NADP) because their continual switching between reduced (NAD(P)H) and oxidized (NAD(P)+) forms is involved in the modulation of redox signaling and the determination of the reducing power and further antioxidant responses. Norway maple and sycamore seeds representing the orthodox and recalcitrant categories, respectively, were used as models in a comparison of responses to water loss. The process of desiccation up to 10% water content (WC) was monitored in Norway maple seeds, while dehydration up to 30% WC was monitored in desiccation-sensitive sycamore seeds. Norway maple and sycamore seeds, particularly their embryonic axes, exhibited a distinct redox status during dehydration and desiccation. High NADPH levels, NAD+ accumulation, low and stable NAD(P)H/NAD(P)+ ratios expressed as reducing power and high NADPH-dependent enzyme activity were reported in Norway maple seeds and were considered attributes of orthodox-type seeds. The contrasting results of sycamore seeds contributed to their low antioxidant capacity and high sensitivity to desiccation. NADPH deficiency, low NADPH-dependent enzyme activity and lack of NAD+ accumulation were primary features of sycamore seeds, with implications for their NAD(P)H/NAD(P)+ ratios and reducing power and with effects on many seed traits. Thus, we propose that the distinct levels of pyridine nucleotides and their redox status contribute to orthodox and recalcitrant phenotype differentiation in seeds by affecting cellular redox signaling, metabolism and the antioxidant system.
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Affiliation(s)
- Shirin Alipour
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
- Department of Forestry, Faculty of Agriculture and Natural Resources, Lorestan University, Khorramabad, Iran
| | - Natalia Wojciechowska
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Ewelina Stolarska
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Karolina Bilska
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Ewa Marzena Kalemba
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
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18
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Lin CT, Xu T, Xing SL, Zhao L, Sun RZ, Liu Y, Moore JP, Deng X. Weighted Gene Co-expression Network Analysis (WGCNA) Reveals the Hub Role of Protein Ubiquitination in the Acquisition of Desiccation Tolerance in Boea hygrometrica. PLANT & CELL PHYSIOLOGY 2019; 60:2707-2719. [PMID: 31410481 DOI: 10.1093/pcp/pcz160] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 08/06/2019] [Indexed: 05/28/2023]
Abstract
Boea hygrometrica can survive extreme drought conditions and has been used as a model to study desiccation tolerance. A genome-wide transcriptome analysis of B. hygrometrica showed that the plant can survive rapid air-drying after experiencing a slow soil-drying acclimation phase. In addition, a weighted gene co-expression network analysis was used to study the transcriptomic datasets. A network comprising 22 modules was constructed, and seven modules were found to be significantly related to desiccation response using an enrichment analysis. Protein ubiquitination was observed to be a common process linked to hub genes in all the seven modules. Ubiquitin-modified proteins with diversified functions were identified using immunoprecipitation coupled with mass spectrometry. The lowest level of ubiquitination was noted at the full soil drying priming stage, which coincided the accumulation of dehydration-responsive gene BhLEA2. The highly conserved RY motif (CATGCA) was identified from the promoters of ubiquitin-related genes that were downregulated in the desiccated samples. An in silico gene expression analysis showed that the negative regulation of ubiquitin-related genes is potentially mediated via a B3 domain-containing transcription repressor VAL1. This study suggests that priming may involve the transcriptional regulation of several major processes, and the transcriptional regulation of genes in protein ubiquitination may play a hub role to deliver acclimation signals to posttranslational level in the acquisition of desiccation tolerance in B. hygrometrica.
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Affiliation(s)
- Chih-Ta Lin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Tao Xu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Shi-Lai Xing
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Li Zhao
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Run-Ze Sun
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Yang Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - John Paul Moore
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Matieland 7602, South Africa
| | - Xin Deng
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
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19
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Alabdullah AK, Borrill P, Martin AC, Ramirez-Gonzalez RH, Hassani-Pak K, Uauy C, Shaw P, Moore G. A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization. FRONTIERS IN PLANT SCIENCE 2019; 10:1325. [PMID: 31681395 PMCID: PMC6813927 DOI: 10.3389/fpls.2019.01325] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/24/2019] [Indexed: 05/05/2023]
Abstract
Polyploidization has played an important role in plant evolution. However, upon polyploidization, the process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a single copy following whole genome duplication to stabilize the polyploid genome. Therefore, upon the polyploidization of wheat, a hexaploid species with three related (homeologous) genomes, the stabilization process may have involved rapid changes in content and expression of MGs on homeologous chromosomes (homeologs). To examine this hypothesis, sets of candidate MGs were identified in wheat using co-expression network analysis and orthology informed approaches. In total, 130 RNA-Seq samples from a range of tissues including wheat meiotic anthers were used to define co-expressed modules of genes. Three modules were significantly correlated with meiotic tissue samples but not with other tissue types. These modules were enriched for GO terms related to cell cycle, DNA replication, and chromatin modification and contained orthologs of known MGs. Overall, 74.4% of genes within these meiosis-related modules had three homeologous copies which was similar to other tissue-related modules. Amongst wheat MGs identified by orthology, rather than co-expression, the majority (93.7%) were either retained in hexaploid wheat at the same number of copies (78.4%) or increased in copy number (15.3%) compared to ancestral wheat species. Furthermore, genes within meiosis-related modules showed more balanced expression levels between homeologs than genes in non-meiosis-related modules. Taken together, our results do not support extensive gene loss nor changes in homeolog expression of MGs upon wheat polyploidization. The construction of the MG co-expression network allowed identification of hub genes and provided key targets for future studies.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | | | | | - Keywan Hassani-Pak
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Peter Shaw
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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20
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Dehydration Sensitivity at the Early Seedling Establishment Stages of the European Beech (Fagus sylvatica L.). FORESTS 2019. [DOI: 10.3390/f10100900] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Shortage of water is a limiting factor for the growth and development of plants, particularly at early developmental stages. We focused on the European beech (Fagus sylvatica L.), which produces seeds and further seedlings in large intervals of up to ten years. To explore the beech seedling establishment process, six stages referring to embryo expansion were studied to determine sensitivity to dehydration. The characterization of the response of elongating embryonic axes and cotyledons included a viability test before and after dehydration and measurement of the amounts of electrolyte leakage, concentration, and arrangement of storage materials, changes in chaperone proteins related to water deficit, and accumulation of hydrogen peroxide and superoxide anion radicals. Elongating embryonic axes and cotyledons differed in water content, dehydration rates, membrane permeability before and after dehydration, protein, and lipid decomposition pattern, and amount of 44-kDa dehydrin and 22-kDa small heat shock protein (sHSP). Protruding embryonic axes were more sensitive to dehydration than cotyledons, although dehydration caused transient reinduction of three dehydrin-like proteins and sHSP synthesis, which accompany desiccation tolerance. Extended deterioration, including overproduction of hydrogen peroxide and depletion of superoxide anion radicals, was reported in dehydrated embryonic axes longer than 10 mm characterized by highly elevated cellular leakage. The apical part elongating embryonic axes consisting of the radicles was the most sensitive part of the seed to dehydration, and the root apical meristem area was the first to become inviable. The effects of severe dehydration involving ROS imbalance and reduced viability in beech seedlings with embryonic axes longer than 10 mm might help to explain the difficulties in beech seedling establishment observed in drought-affected environments. The conversion of environmental drought into climate-originated oxidative stress affecting beech seedling performance is discussed in this report.
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Cui Q, Li Y, He X, Li S, Zhong X, Liu B, Zhang D, Li Q. Physiological and iTRAQ based proteomics analyses reveal the mechanism of elevated CO 2 concentration alleviating drought stress in cucumber (Cucumis sativus L.) seedlings. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:142-153. [PMID: 31493674 DOI: 10.1016/j.plaphy.2019.08.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Carbon dioxide is one of the most important anthropogenic greenhouse gases. We previously confirmed that elevated [CO2] alleviated the negative consequences of drought stress to cucumber seedlings, but the physiological mechanism remains unknown. We investigated the morphological and physiological characteristics as well as iTRAQ-based proteomics analyses in this study under different combinations [CO2] (400 and (800 ± 20) μmol·mol-1) and water conditions (no, moderate and severe drought stress simulated by polyethylene glycol 6000). The results showed: (1) elevated [CO2] significantly increased plant height, stem diameter, leaf area and relative water content (RWC) under drought stress; (2) drought stress significantly increased J and K peaks of the chlorophyll a fluorescence transient, indicating the damage of photosynthetic electron transport chain, while elevated [CO2] decreased them especially under moderate drought condition; (3) iTRAQ-based proteomics analyses indicated that elevated [CO2] increased the abundance of psbJ and the PSI reaction center subunit VI-2 in seedlings exposed to moderate drought stress; (4) the abundance of uroporphyrinogen decarboxylase 2 and tetrapyrrole-binding protein decreased in response to elevated [CO2] under severe drought condition; (5) elevated [CO2] regulated the expression of chloroplast proteins such as those related to stress and defense response, redox homeostasis, metabolic pathways. In conclusion, elevated [CO2] enhanced the efficiency of photosynthetic electron transport, limited the absorption of excess light energy, enhanced the ability of antioxidant and osmotic adjustment, and alleviated the accumulation of toxic substances under drought stress. These findings provide new clues for understanding the molecular basis of elevated [CO2] alleviated plant drought stress.
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Affiliation(s)
- Qingqing Cui
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Bei'jing, 100081, China
| | - Yiman Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Xinrui He
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Shuhao Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Xin Zhong
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Binbin Liu
- State Key Laboratory of Crop Biology, Tai'an, 271018, China
| | - Dalong Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Tai'an, 271018, China.
| | - Qingming Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Tai'an, 271018, China.
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22
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Marques A, Nijveen H, Somi C, Ligterink W, Hilhorst H. Induction of desiccation tolerance in desiccation sensitive Citrus limon seeds. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:624-638. [PMID: 30697936 PMCID: PMC6593971 DOI: 10.1111/jipb.12788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/25/2019] [Indexed: 05/03/2023]
Abstract
Many economically important perennial species bear recalcitrant seeds, including tea, coffee, cocoa, mango, citrus, rubber, oil palm and coconut. Orthodox seeds can be dried almost completely without losing viability, but so-called recalcitrant seeds have a very limited storage life and die upon drying below a higher critical moisture content than orthodox seeds. As a result, the development of long-term storage methods for recalcitrant seeds is compromised. Lowering this critical moisture content would be very valuable since dry seed storage is the safest, most convenient and cheapest method for conserving plant genetic resources. Therefore, we have attempted to induce desiccation tolerance (DT) in the desiccation sensitive seeds of Citrus limon. We show that DT can be induced by paclobutrazol (an inhibitor of gibberellin biosynthesis) and we studied its associated transcriptome to delineate the molecular mechanisms underlying this induction of DT. Paclobutrazol not only interfered with gibberellin related gene expression but also caused extensive changes in expression of genes involved in the biosynthesis and signaling of other hormones. Paclobutrazol induced a transcriptomic switch encompassing suppression of biotic- and induction of abiotic responses. We hypothesize that this is the main driver of the induction of DT by paclobutrazol in C. limon seeds.
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Affiliation(s)
- Alexandre Marques
- Laboratory of Plant PhysiologyWageningen University and ResearchWageningenThe Netherlands
| | - Harm Nijveen
- Laboratory of Plant PhysiologyWageningen University and ResearchWageningenThe Netherlands
- Bioinformatics GroupWageningen University and ResearchWageningenThe Netherlands
| | - Charles Somi
- Laboratory of Plant PhysiologyWageningen University and ResearchWageningenThe Netherlands
| | - Wilco Ligterink
- Laboratory of Plant PhysiologyWageningen University and ResearchWageningenThe Netherlands
| | - Henk Hilhorst
- Laboratory of Plant PhysiologyWageningen University and ResearchWageningenThe Netherlands
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23
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Takeda S, Ochiai K, Kagaya Y, Egusa W, Morimoto H, Sakazono S, Osaka M, Nabemoto M, Suzuki G, Watanabe M, Suwabe K. Abscisic acid-mediated developmental flexibility of stigmatic papillae in response to ambient humidity in Arabidopsis thaliana. Genes Genet Syst 2018; 93:209-220. [PMID: 30473573 DOI: 10.1266/ggs.18-00025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Stigmatic papillae develop at the apex of the gynoecium and play an important role as a site of pollination. The papillae in Brassicaceae are of the dry and unicellular type, and more than 15,000 genes are expressed in the papillae; however, the molecular and physiological mechanisms of their development remain unknown. We found that the papillae in Arabidopsis thaliana change their length in response to altered ambient humidity: papillae of flowers incubated under high humidity elongated more than those under normal humidity conditions. Genetic analysis and transcriptome data suggest that an abscisic acid-mediated abiotic stress response mechanism regulates papilla length. Our data suggest a flexible regulation of papilla elongation at the post-anthesis stage, in response to abiotic stress, as an adaptation to environmental conditions.
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Affiliation(s)
- Seiji Takeda
- Laboratory of Cell and Genome Biology, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University.,Laboratory of Cell and Genome Biology, Biotechnology Research Department, Kyoto Prefectural Agriculture Forestry and Fisheries Technology Center
| | - Kohki Ochiai
- Laboratory of Cell and Genome Biology, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
| | - Yasuaki Kagaya
- Laboratory of Plant Functional Genomics, Life Science Research Center, Mie University.,Laboratory of Plant Functional Genomics, Graduate School of Regional Innovation Studies, Mie University
| | - Wataru Egusa
- Laboratory of Molecular Genetics and Breeding, Graduate School of Bioresources, Mie University
| | - Hiroaki Morimoto
- Laboratory of Molecular Genetics and Breeding, Graduate School of Bioresources, Mie University
| | - Satomi Sakazono
- Laboratory of Plant Molecular Breeding, Graduate School of Life Sciences, Tohoku University
| | - Masaaki Osaka
- Laboratory of Plant Molecular Breeding, Graduate School of Life Sciences, Tohoku University
| | - Moe Nabemoto
- Laboratory of Plant Molecular Breeding, Graduate School of Life Sciences, Tohoku University
| | - Go Suzuki
- Laboratory of Plant Molecular Genetics, Division of Natural Science, Osaka Kyoiku University
| | - Masao Watanabe
- Laboratory of Plant Molecular Breeding, Graduate School of Life Sciences, Tohoku University
| | - Keita Suwabe
- Laboratory of Molecular Genetics and Breeding, Graduate School of Bioresources, Mie University
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24
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Marques A, Buijs G, Ligterink W, Hilhorst H. Evolutionary ecophysiology of seed desiccation sensitivity. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:1083-1095. [PMID: 32290970 DOI: 10.1071/fp18022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/11/2018] [Indexed: 05/28/2023]
Abstract
Desiccation sensitive (DS) seeds do not survive dry storage due to their lack of desiccation tolerance. Almost half of the plant species in tropical rainforests produce DS seeds and therefore the desiccation sensitivity of these seeds represents a problem for and long-term biodiversity conservation. This phenomenon raises questions as to how, where and why DS (desiccation sensitive)-seeded species appeared during evolution. These species evolved probably independently from desiccation tolerant (DT) seeded ancestors. They adapted to environments where the conditions are conducive to immediate germination after shedding, e.g. constant and abundant rainy seasons. These very predictable conditions offered a relaxed selection for desiccation tolerance that eventually got lost in DS seeds. These species are highly dependent on their environment to survive and they are seriously threatened by deforestation and climate change. Understanding of the ecology, evolution and molecular mechanisms associated with seed desiccation tolerance can shed light on the resilience of DS-seeded species and guide conservation efforts. In this review, we survey the available literature for ecological and physiological aspects of DS-seeded species and combine it with recent knowledge obtained from DT model species. This enables us to generate hypotheses concerning the evolution of DS-seeded species and their associated genetic alterations.
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Affiliation(s)
- Alexandre Marques
- Laboratory of Plant Physiology, Wageningen University and Research, PO Box 16, 6700AA Wageningen, The Netherlands
| | - Gonda Buijs
- Laboratory of Plant Physiology, Wageningen University and Research, PO Box 16, 6700AA Wageningen, The Netherlands
| | - Wilco Ligterink
- Laboratory of Plant Physiology, Wageningen University and Research, PO Box 16, 6700AA Wageningen, The Netherlands
| | - Henk Hilhorst
- Laboratory of Plant Physiology, Wageningen University and Research, PO Box 16, 6700AA Wageningen, The Netherlands
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25
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iTRAQ-based quantitative proteomic analysis reveals pathways associated with re-establishing desiccation tolerance in germinating seeds of Caragana korshinskii Kom. J Proteomics 2018; 179:1-16. [DOI: 10.1016/j.jprot.2018.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/09/2018] [Accepted: 01/17/2018] [Indexed: 01/04/2023]
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26
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Xu LX, Lin YX, Wang LH, Zhou YC. Dehiscence method: a seed-saving, quick and simple viability assessment in rice. PLANT METHODS 2018; 14:68. [PMID: 30116291 PMCID: PMC6085679 DOI: 10.1186/s13007-018-0334-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/30/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND Seed viability monitoring is very important in ex situ germplasm preservation to detect germplasm deterioration. This requires seed-, time- and labor- saving methods with high precision to assess seed germination as viability. Although the current non-invasive, rapid, sensing methods (NRSs) are time- and labor-saving, they lack the precision and simplicity which are the virtues of traditional germination. Moreover, they consume a considerable amount of seeds to adjust sensed signals to germination percentage, which disregards the seed-saving objective. This becomes particularly severe for rare or endangered species whose seeds are already scarce. Here we propose a new method that is precise, low-invasive, simple, and quick, which involves analyzing the pattern of dehiscence (seed coat rupture), followed by embryonic protrusion. RESULTS Dehiscence proved simple to identify. After the trial of 20 treatments from 3 rice varieties, we recognized that dehiscence percentage at the 48th hour of germination (D(48)) correlates significantly with germination rate for tested seed lots. In addition, we found that the final germination percentage corresponded to D(48) plus 5. More than 70% of the seeds survived post-dehiscence desiccation for storage. Hydrogen peroxide (1 mM) as the solution for imbibition could further improve the survival. The method also worked quicker than tetrazolium which is honored as a fast, traditional method, in detecting less vigorous but viable seeds. CONCLUSION We demonstrated the comprehensive virtues of dehiscence method in assessing rice seed: it is more precise and easier to use than NRSs and is faster and more seed-saving than traditional methods. We anticipate modifications including artificial intelligence to extend our method to increasingly diverse circumstances and species.
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Affiliation(s)
- Ling-xiang Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002 People’s Republic of China
- National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 People’s Republic of China
| | - Yi-xin Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002 People’s Republic of China
- National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 People’s Republic of China
| | - Li-hong Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122 People’s Republic of China
| | - Yuan-chang Zhou
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002 People’s Republic of China
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27
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Costa MCD, Cooper K, Hilhorst HWM, Farrant JM. Orthodox Seeds and Resurrection Plants: Two of a Kind? PLANT PHYSIOLOGY 2017; 175:589-599. [PMID: 28851758 PMCID: PMC5619911 DOI: 10.1104/pp.17.00760] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/22/2017] [Indexed: 05/27/2023]
Abstract
Understanding shared strategies for desiccation tolerance in orthodox seeds and resurrection plants can yield insights for agricultural improvement.
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Affiliation(s)
- Maria-Cecília D Costa
- Department of Molecular and Cell Biology, University of Cape Town, 7701 Cape Town, South Africa
| | - Keren Cooper
- Department of Molecular and Cell Biology, University of Cape Town, 7701 Cape Town, South Africa
| | - Henk W M Hilhorst
- Laboratory of Plant Physiology, Wageningen University, 6708PB Wageningen, The Netherlands
| | - Jill M Farrant
- Department of Molecular and Cell Biology, University of Cape Town, 7701 Cape Town, South Africa
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28
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Giarola V, Hou Q, Bartels D. Angiosperm Plant Desiccation Tolerance: Hints from Transcriptomics and Genome Sequencing. TRENDS IN PLANT SCIENCE 2017; 22:705-717. [PMID: 28622918 DOI: 10.1016/j.tplants.2017.05.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/12/2017] [Accepted: 05/18/2017] [Indexed: 05/21/2023]
Abstract
Desiccation tolerance (DT) in angiosperms is present in the small group of resurrection plants and in seeds. DT requires the presence of protective proteins, specific carbohydrates, restructuring of membrane lipids, and regulatory mechanisms directing a dedicated gene expression program. Many components are common to resurrection plants and seeds; however, some are specific for resurrection plants. Understanding how each component contributes to DT is challenging. Recent transcriptome analyses and genome sequencing indicate that increased expression is essential of genes encoding protective components, recently evolved, species-specific genes and non-protein-coding RNAs. Modification and reshuffling of existing cis-regulatory promoter elements seems to play a role in the rewiring of regulatory networks required for increased expression of DT-related genes in resurrection species.
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Affiliation(s)
- Valentino Giarola
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Quancan Hou
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115 Bonn, Germany; Present address: Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115 Bonn, Germany.
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29
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Peng L, Lang S, Wang Y, Pritchard HW, Wang X. Modulating role of ROS in re-establishing desiccation tolerance in germinating seeds of Caragana korshinskii Kom. JOURNAL OF EXPERIMENTAL BOTANY 2017. [PMID: 28633353 DOI: 10.1093/jxb/erx172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In close agreement with visible germination, orthodox seeds lose desiccation tolerance (DT). This trait can be regained under osmotic stress, but the mechanisms are poorly understood. In this study, germinating seeds of Caragana korshinskii Kom. were investigated, focusing on the potential modulating roles of reactive oxygen species (ROS) in the re-establishment of DT. Germinating seeds with 2 mm long radicles can be rendered tolerant to desiccation by incubation in a polyethylene glycol (PEG) solution (-1.7 MPa). Upon PEG incubation, ROS accumulation was detected in the radicles tip by nitroblue tetrazolium chloride staining and further confirmed by confocal microscopy. The PEG-induced re-establishment of DT was repressed when ROS scavengers were added to the PEG solution. Moreover, ROS act downstream of abscisic acid (ABA) to modulate PEG-mediated re-establishment of DT and serve as a new inducer to re-establish DT. Transcriptomic analysis revealed that re-establishment of DT by ROS involves the up-regulation of key genes in the phenylpropanoid-flavonoid pathway, and total flavonoid content and key enzyme activity increased after ROS treatment. Furthermore, DT was repressed by an inhibitor of phenylalanine ammonia lyase. Our data suggest that ROS play a key role in the re-establishment of DT by regulating stress-related genes and the phenylpropanoid-flavonoid pathway.
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Affiliation(s)
- Long Peng
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Tsinghua East Road, Beijing, China
| | - Sirui Lang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Tsinghua East Road, Beijing, China
| | - Yu Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Tsinghua East Road, Beijing, China
| | - Hugh W Pritchard
- Royal Botanic Gardens, Kew, Wellcome Trust Millennium Building, Wakehurst Place, Ardingly RH17 6TN, UK
| | - Xiaofeng Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Tsinghua East Road, Beijing, China
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30
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Rai A, Saito K, Yamazaki M. Integrated omics analysis of specialized metabolism in medicinal plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:764-787. [PMID: 28109168 DOI: 10.1111/tpj.13485] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 05/19/2023]
Abstract
Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.
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Affiliation(s)
- Amit Rai
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
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31
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Leprince O, Pellizzaro A, Berriri S, Buitink J. Late seed maturation: drying without dying. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:827-841. [PMID: 28391329 DOI: 10.1093/jxb/erw363] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Besides the deposition of storage reserves, seed maturation is characterized by the acquisition of functional traits including germination, desiccation tolerance, dormancy, and longevity. After seed filling, seed longevity increases up to 30-fold, concomitant with desiccation that brings the embryo to a quiescent state. The period that we define as late maturation phase can represent 10-78% of total seed development time, yet it remains overlooked. Its importance is underscored by the fact that in the seed production chain, the stage of maturity at harvest is the primary factor that influences seed longevity and seedling establishment. This review describes the major events and regulatory pathways underlying the acquisition of seed longevity, focusing on key indicators of maturity such as chlorophyll degradation, accumulation of raffinose family oligosaccharides, late embryogenesis abundant proteins, and heat shock proteins. We discuss how these markers are correlated with or contribute to seed longevity, and highlight questions that merit further attention. We present evidence suggesting that molecular players involved in biotic defence also have a regulatory role in seed longevity. We also explore how the concept of plasticity can help understand the acquisition of longevity.
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Affiliation(s)
- Olivier Leprince
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 Quasav, 42 rue George Morel, 49071 Beaucouzé, France
| | - Anthoni Pellizzaro
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 Quasav, 42 rue George Morel, 49071 Beaucouzé, France
| | - Souha Berriri
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 Quasav, 42 rue George Morel, 49071 Beaucouzé, France
| | - Julia Buitink
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 Quasav, 42 rue George Morel, 49071 Beaucouzé, France
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32
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Costa MCD, Farrant JM, Oliver MJ, Ligterink W, Buitink J, Hilhorst HMW. Key genes involved in desiccation tolerance and dormancy across life forms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 251:162-168. [PMID: 27593474 DOI: 10.1016/j.plantsci.2016.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/27/2016] [Accepted: 02/01/2016] [Indexed: 05/25/2023]
Abstract
Desiccation tolerance (DT, the ability of certain organisms to survive severe dehydration) was a key trait in the evolution of life in terrestrial environments. Likely, the development of desiccation-tolerant life forms was accompanied by the acquisition of dormancy or a dormancy-like stage as a second powerful adaptation to cope with variations in the terrestrial environment. These naturally stress tolerant life forms may be a good source of genetic information to generate stress tolerant crops to face a future with predicted higher occurrence of drought. By mining for key genes and mechanisms related to DT and dormancy conserved across different species and life forms, unique candidate key genes may be identified. Here we identify several of these putative key genes, shared among multiple organisms, encoding for proteins involved in protection, growth and energy metabolism. Mutating a selection of these genes in the model plant Arabidopsis thaliana resulted in clear DT-, dormancy- and other seed-associated phenotypes, showing the efficiency and power of our approach and paves the way for the development of drought-stress tolerant crops. Our analysis supports a co-evolution of DT and dormancy by shared mechanisms that favour survival and adaptation to ever-changing environments with strong seasonal fluctuations.
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Affiliation(s)
- Maria Cecília D Costa
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Jill M Farrant
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
| | - Melvin J Oliver
- U.S. Department of Agriculture-ARS-MWA-PGRU, 205 Curtis Hall, University of Missouri, Columbia, MO 65211, USA
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Julia Buitink
- Institut National de la Recherch Agronomique, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Qualité et Santé du Végétal, 49045 Angers, France
| | - Henk M W Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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33
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Construction of co-expression network based on natural expression variation of xylogenesis-related transcripts in Eucalyptus tereticornis. Mol Biol Rep 2016; 43:1129-46. [DOI: 10.1007/s11033-016-4046-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 07/20/2016] [Indexed: 12/23/2022]
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34
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Tian X, Li S, Liu Y, Liu X. Transcriptomic Profiling Reveals Metabolic and Regulatory Pathways in the Desiccation Tolerance of Mungbean ( Vigna radiata [L.] R. Wilczek). FRONTIERS IN PLANT SCIENCE 2016; 7:1921. [PMID: 28066476 PMCID: PMC5174128 DOI: 10.3389/fpls.2016.01921] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/05/2016] [Indexed: 05/20/2023]
Abstract
Mungbean (Vigna radiate L. Wilczek) is an important legume crop for its valuable nutritional and health benefits. Desiccation tolerance (DT) is a capacity of seeds to survive and maintain physiological activities during storage and under stress conditions. Many studies of DT have been reported in other legume crop, such as soybean and Medicago truncatula with little studies in the mungbean. In this study, the transcript profiles of mungbean seeds under different imbibition times were investigated for DT using RNA-sequencing (RNA-seq). A total of 3210 differentially expressed genes (DEGs) were found at the key period of DT (3-18 h of imbibition). Gene ontology (GO) and KEGG analysis showed that the terms of "response to stimulus," "transcription regulator," "methylation," and "starch and sucrose metabolism" were enriched for DT. Clustering analysis also showed that many transcription factors (MYB, AP2, and NAC), HSPs, embryogenesis abundant (LEA) proteins, and genes encoding methyltransferase and histone were differentially expressed. Nine of these DEGs were further validated by quantitative RT-PCR (qRT-PCR). Our study extends our knowledge of mungbean transcriptomes and further provides insight into the molecular mechanism of DT as well as new strategies for developing drought-tolerant crops.
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Affiliation(s)
- Xiangrong Tian
- College of Biology, Hunan UniversityChangsha, China
- Key Laboratory of Plant Resource Conservation and Utilization of Hunan Province, Jishou UniversityJishou, China
- *Correspondence: Xiangrong Tian
| | - Sidi Li
- Key Laboratory of Plant Resource Conservation and Utilization of Hunan Province, Jishou UniversityJishou, China
| | - Yisong Liu
- Center of Analytical Service, Hunan Agricultural UniversityChangsha, China
| | - Xuanming Liu
- College of Biology, Hunan UniversityChangsha, China
- Xuanming Liu
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Serin EAR, Nijveen H, Hilhorst HWM, Ligterink W. Learning from Co-expression Networks: Possibilities and Challenges. FRONTIERS IN PLANT SCIENCE 2016; 7:444. [PMID: 27092161 PMCID: PMC4825623 DOI: 10.3389/fpls.2016.00444] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/21/2016] [Indexed: 05/18/2023]
Abstract
Plants are fascinating and complex organisms. A comprehensive understanding of the organization, function and evolution of plant genes is essential to disentangle important biological processes and to advance crop engineering and breeding strategies. The ultimate aim in deciphering complex biological processes is the discovery of causal genes and regulatory mechanisms controlling these processes. The recent surge of omics data has opened the door to a system-wide understanding of the flow of biological information underlying complex traits. However, dealing with the corresponding large data sets represents a challenging endeavor that calls for the development of powerful bioinformatics methods. A popular approach is the construction and analysis of gene networks. Such networks are often used for genome-wide representation of the complex functional organization of biological systems. Network based on similarity in gene expression are called (gene) co-expression networks. One of the major application of gene co-expression networks is the functional annotation of unknown genes. Constructing co-expression networks is generally straightforward. In contrast, the resulting network of connected genes can become very complex, which limits its biological interpretation. Several strategies can be employed to enhance the interpretation of the networks. A strategy in coherence with the biological question addressed needs to be established to infer reliable networks. Additional benefits can be gained from network-based strategies using prior knowledge and data integration to further enhance the elucidation of gene regulatory relationships. As a result, biological networks provide many more applications beyond the simple visualization of co-expressed genes. In this study we review the different approaches for co-expression network inference in plants. We analyse integrative genomics strategies used in recent studies that successfully identified candidate genes taking advantage of gene co-expression networks. Additionally, we discuss promising bioinformatics approaches that predict networks for specific purposes.
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Affiliation(s)
- Elise A. R. Serin
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Harm Nijveen
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
- Laboratory of Bioinformatics, Wageningen UniversityWageningen, Netherlands
| | - Henk W. M. Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
- *Correspondence: Wilco Ligterink
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Leprince O, Buitink J. Introduction to desiccation biology: from old borders to new frontiers. PLANTA 2015; 242:369-78. [PMID: 26142353 DOI: 10.1007/s00425-015-2357-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 06/22/2015] [Indexed: 05/21/2023]
Abstract
A special issue reviews the recent progress made in our understanding of desiccation tolerance across various plant and animal kingdoms. It has been known for a long time that seeds can survive near absolute protoplasmic dehydration through air drying and complete germination upon rehydration because of their desiccation tolerance. This property is present both in prokaryotes and eukaryotes across all life kingdoms. These dry organisms suspend their metabolism when dry, are extremely tolerant to acute environmental stresses and are relatively stable during long periods of desiccation. Studies aiming at understanding the mechanisms of survival in the dry state have emerged during the past 40 years, moving from in vitro to genomic models and comparative genomics, and from a view that tolerance is an all-or-nothing phenomenon to a quantitative trait. With the prospect of global climate change, understanding the mechanisms of desiccation tolerance appears to be a promising avenue as a prelude to engineering crops for improved drought tolerance. Understanding desiccation is also useful for seed banks that rely on dehydration tolerance to preserve plant genetic resources in the form of these propagules. Articles in this special issue explore the recent progress in our understanding of desiccation tolerance, including the evolutionary mechanisms that have been adopted across various plant (algae, lichens, seeds, resurrection plants) and animal model systems (Caenorhabditis elegans, brine shrimp). We propose that the term desiccation biology defines the discipline dedicated to understand the desiccation tolerance in living organisms as well as the limits and time constraints thereof.
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Affiliation(s)
- Olivier Leprince
- Agrocampus Ouest, Institut de Recherche en Horticulture et Semences, UMR 1345, Campus du Végétal, 42 rue Georges Morel, CS 60057, 49071, Beaucouzé, France,
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Costa MCD, Nijveen H, Ligterink W, Buitink J, Hilhorst HW. Time-series analysis of the transcriptome of the re-establishment of desiccation tolerance by ABA in germinated Arabidopsis thaliana seeds. GENOMICS DATA 2015; 5:154-6. [PMID: 26484244 PMCID: PMC4583984 DOI: 10.1016/j.gdata.2015.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 11/21/2022]
Abstract
Expression analyses of time series have become a very popular method for studying the dynamics of a wide range of biological processes. Here, we present expression analysis of a time series with the help of microarrays used to study the re-establishment of desiccation tolerance (DT) in germinated Arabidopsis thaliana seeds. Mature seeds of A. thaliana are desiccation tolerant (survive the loss of most of their water content), but they become desiccation sensitive while progressing to germination. Yet, there is a small developmental window during which DT can be re-established by treatment with the plant hormone abscisic acid (ABA). We studied germinated A. thaliana seeds at the stage of radicle protrusion during ABA incubation for 0 h, 2 h, 12 h, 24 h and 72 h. We describe in detail the methodology applied for generating and analyzing this expression data of time series. The microarray raw data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62876) may be valuable for further studies on this experimental system, such as the construction of a gene co-expression network [1].
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