1
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Sybilska E, Collin A, Sadat Haddadi B, Mur LAJ, Beckmann M, Guo W, Simpson CG, Daszkowska-Golec A. The cap-binding complex modulates ABA-responsive transcript splicing during germination in barley (Hordeum vulgare). Sci Rep 2024; 14:18278. [PMID: 39107424 PMCID: PMC11303550 DOI: 10.1038/s41598-024-69373-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024] Open
Abstract
To decipher the molecular bases governing seed germination, this study presents the pivotal role of the cap-binding complex (CBC), comprising CBP20 and CBP80, in modulating the inhibitory effects of abscisic acid (ABA) in barley. Using both single and double barley mutants in genes encoding the CBC, we revealed that the double mutant hvcbp20.ab/hvcbp80.b displays ABA insensitivity, in stark contrast to the hypersensitivity observed in single mutants during germination. Our comprehensive transcriptome and metabolome analysis not only identified significant alterations in gene expression and splicing patterns but also underscored the regulatory nexus among CBC, ABA, and brassinosteroid (BR) signaling pathways.
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Affiliation(s)
- Ewa Sybilska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | - Anna Collin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | | | - Luis A J Mur
- Department of Life Science, Aberystwyth University, Aberystwyth, UK
| | - Manfred Beckmann
- Department of Life Science, Aberystwyth University, Aberystwyth, UK
| | - Wenbin Guo
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Craig G Simpson
- Cell and Molecular Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland.
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2
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Díez AR, Szakonyi D, Lozano-Juste J, Duque P. Alternative splicing as a driver of natural variation in abscisic acid response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:9-27. [PMID: 38659400 DOI: 10.1111/tpj.16773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Abscisic acid (ABA) is a crucial player in plant responses to the environment. It accumulates under stress, activating downstream signaling to implement molecular responses that restore homeostasis. Natural variance in ABA sensitivity remains barely understood, and the ABA pathway has been mainly studied at the transcriptional level, despite evidence that posttranscriptional regulation, namely, via alternative splicing, contributes to plant stress tolerance. Here, we identified the Arabidopsis accession Kn-0 as less sensitive to ABA than the reference Col-0, as shown by reduced effects of the hormone on seedling establishment, root branching, and stomatal closure, as well as by decreased induction of ABA marker genes. An in-depth comparative transcriptome analysis of the ABA response in the two variants revealed lower expression changes and fewer genes affected for the least ABA-sensitive ecotype. Notably, Kn-0 exhibited reduced levels of the ABA-signaling SnRK2 protein kinases and lower basal expression of ABA-reactivation genes, consistent with our finding that Kn-0 contains less endogenous ABA than Col-0. ABA also markedly affected alternative splicing, primarily intron retention, with Kn-0 being less responsive regarding both the number and magnitude of alternative splicing events, particularly exon skipping. We find that alternative splicing introduces a more ecotype-specific layer of ABA regulation and identify ABA-responsive splicing changes in key ABA pathway regulators that provide a functional and mechanistic link to the differential sensitivity of the two ecotypes. Our results offer new insight into the natural variation of ABA responses and corroborate a key role for alternative splicing in implementing ABA-mediated stress responses.
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Affiliation(s)
- Alba R Díez
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Dóra Szakonyi
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Consejo Superior de Investigaciones Científicas (CSIC), 46022, Valencia, Spain
| | - Paula Duque
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
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3
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Hämälä T, Moore C, Cowan L, Carlile M, Gopaulchan D, Brandrud MK, Birkeland S, Loose M, Kolář F, Koch MA, Yant L. Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nat Commun 2024; 15:5377. [PMID: 38918389 PMCID: PMC11199601 DOI: 10.1038/s41467-024-49679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.
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Affiliation(s)
- Tuomas Hämälä
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland.
| | | | - Laura Cowan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Matthew Carlile
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | | | - Siri Birkeland
- Natural History Museum, University of Oslo, Oslo, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Marcus A Koch
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.
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4
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Muhammad S, Xu X, Zhou W, Wu L. Alternative splicing: An efficient regulatory approach towards plant developmental plasticity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1758. [PMID: 35983878 DOI: 10.1002/wrna.1758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/28/2022] [Accepted: 07/19/2022] [Indexed: 05/13/2023]
Abstract
Alternative splicing (AS) is a gene regulatory mechanism that plants adapt to modulate gene expression (GE) in multiple ways. AS generates alternative isoforms of the same gene following various development and environmental stimuli, increasing transcriptome plasticity and proteome complexity. AS controls the expression levels of certain genes and regulates GE networks that shape plant adaptations through nonsense-mediated decay (NMD). This review intends to discuss AS modulation, from interaction with noncoding RNAs to the established roles of splicing factors (SFs) in response to endogenous and exogenous cues. We aim to gather such studies that highlight the magnitude and impact of AS, which are not always clear from individual articles, when AS is increasing in individual genes and at a global level. This work also anticipates making plant researchers know that AS is likely to occur in their investigations and that dynamic changes in AS and their effects must be frequently considered. We also review our understanding of AS-mediated posttranscriptional modulation of plant stress tolerance and discuss its potential application in crop improvement in the future. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > Splicing Mechanisms RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.
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Affiliation(s)
- Sajid Muhammad
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan, China
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoli Xu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Weijun Zhou
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liang Wu
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan, China
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
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5
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Sybilska E, Daszkowska-Golec A. Alternative splicing in ABA signaling during seed germination. FRONTIERS IN PLANT SCIENCE 2023; 14:1144990. [PMID: 37008485 PMCID: PMC10060653 DOI: 10.3389/fpls.2023.1144990] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Seed germination is an essential step in a plant's life cycle. It is controlled by complex physiological, biochemical, and molecular mechanisms and external factors. Alternative splicing (AS) is a co-transcriptional mechanism that regulates gene expression and produces multiple mRNA variants from a single gene to modulate transcriptome diversity. However, little is known about the effect of AS on the function of generated protein isoforms. The latest reports indicate that alternative splicing (AS), the relevant mechanism controlling gene expression, plays a significant role in abscisic acid (ABA) signaling. In this review, we present the current state of the art about the identified AS regulators and the ABA-related changes in AS during seed germination. We show how they are connected with the ABA signaling and the seed germination process. We also discuss changes in the structure of the generated AS isoforms and their impact on the functionality of the generated proteins. Also, we point out that the advances in sequencing technology allow for a better explanation of the role of AS in gene regulation by more accurate detection of AS events and identification of full-length splicing isoforms.
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Ma SH, He GQ, Navarro-Payá D, Santiago A, Cheng YZ, Jiao JB, Li HJ, Zuo DD, Sun HT, Pei MS, Yu YH, Matus JT, Guo DL. Global analysis of alternative splicing events based on long- and short-read RNA sequencing during grape berry development. Gene 2023; 852:147056. [PMID: 36414171 DOI: 10.1016/j.gene.2022.147056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/21/2022]
Affiliation(s)
- Shuai-Hui Ma
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, China
| | - Guang-Qi He
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, China
| | - David Navarro-Payá
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - Yi-Zhe Cheng
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, China
| | - Jia-Bing Jiao
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, China
| | - Hui-Jie Li
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, China
| | - Ding-Ding Zuo
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, China
| | - Hao-Ting Sun
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, China
| | - Mao-Song Pei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, China
| | - Yi-He Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, China
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - Da-Long Guo
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang 471023, China.
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7
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Kufel J, Diachenko N, Golisz A. Alternative splicing as a key player in the fine-tuning of the immunity response in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2022; 23:1226-1238. [PMID: 35567423 PMCID: PMC9276941 DOI: 10.1111/mpp.13228] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 06/01/2023]
Abstract
Plants, like animals, are constantly exposed to abiotic and biotic stresses, which often inhibit plant growth and development, and cause tissue damage, disease, and even plant death. Efficient and timely response to stress requires appropriate co- and posttranscriptional reprogramming of gene expression. Alternative pre-mRNA splicing provides an important layer of this regulation by controlling the level of factors involved in stress response and generating additional protein isoforms with specific features. Recent high-throughput studies have revealed that several defence genes undergo alternative splicing that is often affected by pathogen infection. Despite extensive work, the exact mechanisms underlying these relationships are still unclear, but the contribution of alternative protein isoforms to the defence response and the role of regulatory factors, including components of the splicing machinery, have been established. Modulation of gene expression in response to stress includes alternative splicing, chromatin remodelling, histone modifications, and nucleosome occupancy. How these processes affect plant immunity is mostly unknown, but these facets open new regulatory possibilities. Here we provide an overview of the current state of knowledge and recent findings regarding the growing importance of alternative splicing in plant response to biotic stress.
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Affiliation(s)
- Joanna Kufel
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
| | - Nataliia Diachenko
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
| | - Anna Golisz
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
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8
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Landi S, Capasso G, Esposito S. Different G6PDH isoforms show specific roles in acclimation to cold stress at various growth stages of barley (Hordeum vulgare) and Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:190-202. [PMID: 34801973 DOI: 10.1016/j.plaphy.2021.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/19/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Low temperatures (0-10 °C) represent a major physiological stress for plants, negatively affecting both their growth rates and overall growth. Cold stress may induce a wide range of negative physiological effects, from oxidative stress to photosynthetic damage. We investigated the effects of low temperatures in two different model plants, Arabidopsis thaliana and Hordeum vulgare. We tested whether the oxidative pentose phosphate pathway (OPPP) is involved in the increase of reductants' levels needed to counteract oxidative stress induced by cold. The expression, occurrence, and activity of different glucose-6-phosphate dehydrogenase (G6PDH, EC 1.1.1.49) isoforms during cold stress and plant recovery from low temperatures, were measured at different growth stages from early germinated to mature pot-grown plants. Our results showed plants exhibited changes in different stress markers; ascorbate peroxidase - APX, catalase - CAT, proline, malondialdehyde, H2O2, NADPH/NADP+. We found that a major role in cold acclimation for cytosolic- and peroxisome-located G6PDHs, and different roles for plastidial/chloroplastic isoforms. This suggests that G6PDH isoforms may regulate redox homeostasis in low temperatures, in order to support the increased and continued demand of reductants during both cold stress and recovery stages. Furthermore, we found a significant involvement of (6PGDH), strengthening the idea that the contribution of the whole oxidative pentose phosphate pathway (OPPP) is required to sustain reductant supply under cold stress.
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Affiliation(s)
- Simone Landi
- Department of Biology, University of Naples Federico II, Complesso Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Giorgia Capasso
- Department of Biology, University of Naples Federico II, Complesso Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Sergio Esposito
- Department of Biology, University of Naples Federico II, Complesso Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy.
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9
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Yang J, Lv W, Shao L, Fu Y, Liu H, Yang C, Chen A, Xie X, Wang Z, Li C. PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species. FRONTIERS IN PLANT SCIENCE 2021; 12:737004. [PMID: 34691113 PMCID: PMC8529222 DOI: 10.3389/fpls.2021.737004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/02/2021] [Indexed: 06/04/2023]
Abstract
In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of single molecular real-time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1,261 AS events in P. trichocarpa and 2,101 in P. ussuriensis among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events, which provided a new insight into the complexity and regulation of AS during cold stress response in different poplar species for the first time.
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Affiliation(s)
- Jingli Yang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Wanqiu Lv
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Liying Shao
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Yanrui Fu
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Haimei Liu
- Biology Group, Jiamusi No.1 High School, Jiamusi, China
| | - Chengjun Yang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Aihua Chen
- Economic Forest Laboratory, Mudanjiang Branch of Heilongjiang Academy of Forestry, Mudanjiang, China
| | - Xieyu Xie
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Zhiwei Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Chenghao Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
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10
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Alternative splicing in plant abiotic stress responses. Biochem Soc Trans 2021; 48:2117-2126. [PMID: 32869832 DOI: 10.1042/bst20200281] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023]
Abstract
Modifications of the cellular proteome pool upon stress allow plants to tolerate environmental changes. Alternative splicing is the most significant mechanism responsible for the production of multiple protein isoforms from a single gene. The spliceosome, a large ribonucleoprotein complex, together with several associated proteins, controls this pre-mRNA processing, adding an additional level of regulation to gene expression. Deep sequencing of transcriptomes revealed that this co- or post-transcriptional mechanism is highly induced by abiotic stress, and concerns vast numbers of stress-related genes. Confirming the importance of splicing in plant stress adaptation, key players of stress signaling have been shown to encode alternative transcripts, whereas mutants lacking splicing factors or associated components show a modified sensitivity and defective responses to abiotic stress. Here, we examine recent literature on alternative splicing and splicing alterations in response to environmental stresses, focusing on its role in stress adaptation and analyzing the future perspectives and directions for research.
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11
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Tognacca RS, Botto JF. Post-transcriptional regulation of seed dormancy and germination: Current understanding and future directions. PLANT COMMUNICATIONS 2021; 2:100169. [PMID: 34327318 PMCID: PMC8299061 DOI: 10.1016/j.xplc.2021.100169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/26/2021] [Accepted: 02/13/2021] [Indexed: 05/06/2023]
Abstract
Seed dormancy is a developmental checkpoint that prevents mature seeds from germinating under conditions that are otherwise favorable for germination. Temperature and light are the most relevant environmental factors that regulate seed dormancy and germination. These environmental cues can trigger molecular and physiological responses including hormone signaling, particularly that of abscisic acid and gibberellin. The balance between the content and sensitivity of these hormones is the key to the regulation of seed dormancy. Temperature and light tightly regulate the transcription of thousands of genes, as well as other aspects of gene expression such as mRNA splicing, translation, and stability. Chromatin remodeling determines specific transcriptional outputs, and alternative splicing leads to different outcomes and produces transcripts that encode proteins with altered or lost functions. Proper regulation of chromatin remodeling and alternative splicing may be highly relevant to seed germination. Moreover, microRNAs are also critical for the control of gene expression in seeds. This review aims to discuss recent updates on post-transcriptional regulation during seed maturation, dormancy, germination, and post-germination events. We propose future prospects for understanding how different post-transcriptional processes in crop seeds can contribute to the design of genotypes with better performance and higher productivity.
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Affiliation(s)
- Rocío Soledad Tognacca
- Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CP1428 Buenos Aires, Argentina
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
| | - Javier Francisco Botto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
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12
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ATHB2 is a negative regulator of germination in Arabidopsis thaliana seeds. Sci Rep 2021; 11:9688. [PMID: 33958633 PMCID: PMC8102570 DOI: 10.1038/s41598-021-88874-5] [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: 02/18/2021] [Accepted: 04/12/2021] [Indexed: 02/03/2023] Open
Abstract
The germination timing of seeds is of the utmost adaptive importance for plant populations. Light is one of the best characterized factors promoting seed germination in several species. The germination is also finely regulated by changes in hormones levels, mainly those of gibberellin (GA) and abscisic acid (ABA). Here, we performed physiological, pharmacological, and molecular analyses to uncover the role of ATHB2, an HD-ZIP II transcription factor, in germination of Arabidopsis seeds. Our study demonstrated that ATHB2 is a negative regulator and sustains the expression of transcription factors to block germination promoted by light. Besides, we found that ATHB2 increases ABA sensitivity. Moreover, ABA and auxin content in athb2-2 mutant is higher than wild-type in dry seeds, but the differences disappeared during the imbibition in darkness and the first hours of exposition to light, respectively. Some ABA and light transcription factors are up-regulated by ATHB2, such as ABI5, ABI3, XERICO, SOMNUS and PIL5/PIF1. In opposition, PIN7, an auxin transport, is down-regulated. The role of ATHB2 as a repressor of germination induced by light affecting the gemination timing, could have differential effects on the establishment of seedlings altering the competitiveness between crops and weeds in the field.
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13
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Fernandez‐Pozo N, Metz T, Chandler JO, Gramzow L, Mérai Z, Maumus F, Mittelsten Scheid O, Theißen G, Schranz ME, Leubner‐Metzger G, Rensing SA. Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:275-293. [PMID: 33453123 PMCID: PMC8641386 DOI: 10.1111/tpj.15161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 05/06/2023]
Abstract
Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA-seq libraries and 136 307 full-length PacBio Iso-seq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At-α polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS-box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full-length transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-β and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni-marburg.de/aetar_db).
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Affiliation(s)
- Noe Fernandez‐Pozo
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
| | - Timo Metz
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
| | - Jake O. Chandler
- School of Biological SciencesRoyal Holloway University of LondonEghamSurreyUK
| | - Lydia Gramzow
- Matthias Schleiden Institute/GeneticsFriedrich Schiller University JenaJenaGermany
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | | | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | - Günter Theißen
- Matthias Schleiden Institute/GeneticsFriedrich Schiller University JenaJenaGermany
| | - M. Eric Schranz
- Biosystematics GroupWageningen UniversityWageningenThe Netherlands
| | - Gerhard Leubner‐Metzger
- School of Biological SciencesRoyal Holloway University of LondonEghamSurreyUK
- Laboratory of Growth RegulatorsCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University and Institute of Experimental BotanyAcademy of Sciences of the Czech RepublicOlomoucCzech Republic
| | - Stefan A. Rensing
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
- BIOSS Centre for Biological Signaling StudiesUniversity of FreiburgFreiburgGermany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO)University of MarburgMarburgGermany
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Thiruppathi D. SPLICEd in the Seeds: Integration of Abscisic Acid and Light Signaling in Arabidopsis. PLANT PHYSIOLOGY 2020; 183:445-446. [PMID: 32493811 PMCID: PMC7271805 DOI: 10.1104/pp.20.00361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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