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Li X, Tang H, Xu T, Wang P, Ma F, Wei H, Fang Z, Wu X, Wang Y, Xue Y, Zhang B. N-terminal acetylation orchestrates glycolate-mediated ROS homeostasis to promote rice thermoresponsive growth. THE NEW PHYTOLOGIST 2024; 243:1742-1757. [PMID: 38934055 DOI: 10.1111/nph.19928] [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: 03/22/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Climate warming poses a significant threat to global crop production and food security. However, our understanding of the molecular mechanisms governing thermoresponsive development in crops remains limited. Here we report that the auxiliary subunit of N-terminal acetyltransferase A (NatA) in rice OsNAA15 is a prerequisite for rice thermoresponsive growth. OsNAA15 produces two isoforms OsNAA15.1 and OsNAA15.2, via temperature-dependent alternative splicing. Among the two, OsNAA15.1 is more likely to form a stable and functional NatA complex with the potential catalytic subunit OsNAA10, leading to a thermoresponsive N-terminal acetylome. Intriguingly, while OsNAA15.1 promotes plant growth under elevated temperatures, OsNAA15.2 exhibits an inhibitory effect. We identified two glycolate oxidases (GLO1/5) as major substrates from the thermoresponsive acetylome. These enzymes are involved in hydrogen peroxide (H2O2) biosynthesis via glycolate oxidation. N-terminally acetylated GLO1/5 undergo their degradation through the ubiquitin-proteasome system. This leads to reduced reactive oxygen species (ROS) production, thereby promoting plant growth, particularly under high ambient temperatures. Conclusively, our findings highlight the pivotal role of N-terminal acetylation in orchestrating the glycolate-mediated ROS homeostasis to facilitate thermoresponsive growth in rice.
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Affiliation(s)
- Xueting Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huashan Tang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ting Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pengfei Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangfang Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haifang Wei
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zi Fang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoyan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanan Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongbiao Xue
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Biyao Zhang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
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2
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Domingo G, Marsoni M, Davide E, Fortunato S, de Pinto MC, Bracale M, Molla G, Gehring C, Vannini C. The cAMP-dependent phosphorylation footprint in response to heat stress. PLANT CELL REPORTS 2024; 43:137. [PMID: 38713285 PMCID: PMC11076351 DOI: 10.1007/s00299-024-03213-y] [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: 02/28/2024] [Accepted: 04/01/2024] [Indexed: 05/08/2024]
Abstract
KEY MESSAGE cAMP modulates the phosphorylation status of highly conserved phosphosites in RNA-binding proteins crucial for mRNA metabolism and reprogramming in response to heat stress. In plants, 3',5'-cyclic adenosine monophosphate (3',5'-cAMP) is a second messenger that modulates multiple cellular targets, thereby participating in plant developmental and adaptive processes. Although its role in ameliorating heat-related damage has been demonstrated, mechanisms that govern cAMP-dependent responses to heat have remained elusive. Here we analyze the role cAMP-dependent phosphorylation during prolonged heat stress (HS) with a view to gain insight into processes that govern plant responses to HS. To do so, we performed quantitative phosphoproteomic analyses in Nicotiana tabacum Bright Yellow-2 cells grown at 27 °C or 35 °C for 3 days overexpressing a molecular "sponge" that reduces free intracellular cAMP levels. Our phosphorylation data and analyses reveal that the presence of cAMP is an essential factor that governs specific protein phosphorylation events that occur during prolonged HS in BY-2 cells. Notably, cAMP modulates HS-dependent phosphorylation of proteins that functions in mRNA processing, transcriptional control, vesicular trafficking, and cell cycle regulation and this is indicative for a systemic role of the messenger. In particular, changes of cAMP levels affect the phosphorylation status of highly conserved phosphosites in 19 RNA-binding proteins that are crucial during the reprogramming of the mRNA metabolism in response to HS. Furthermore, phosphorylation site motifs and molecular docking suggest that some proteins, including kinases and phosphatases, are conceivably able to directly interact with cAMP thus further supporting a regulatory role of cAMP in plant HS responses.
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Affiliation(s)
- Guido Domingo
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy.
| | - Milena Marsoni
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy
| | - Eleonora Davide
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy
| | - Stefania Fortunato
- Department of Biology, University of Bari "Aldo Moro", Piazza Umberto I, 70121, Bari, Italy
| | | | - Marcella Bracale
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy
| | - Gianluca Molla
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX Giugno, 74, 06121, Perugia, Italy
| | - Candida Vannini
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy.
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3
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Ma T, Xu S, Wang Y, Zhang L, Liu Z, Liu D, Jin Z, Pei Y. Exogenous hydrogen sulphide promotes plant flowering through the Arabidopsis splicing factor AtU2AF65a. PLANT, CELL & ENVIRONMENT 2024; 47:1782-1796. [PMID: 38315745 DOI: 10.1111/pce.14849] [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: 10/28/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024]
Abstract
Alternative splicing (AS) is an important regulatory mode at the post-transcriptional level, through which many flowering genes regulate floral transition by producing multiple transcripts, and splicing factors have essential roles in this process. Hydrogen sulphide (H2S) is a newly found gasotransmitter that has critical physiological roles in plants, and one of its potential modes of action is via persulfidation of target proteins at specific cysteine sites. Previously, it has been shown that both the splicing factor AtU2AF65a and H2S are involved in the regulation of plant flowering. This study found that, in Arabidopsis, the promoting effect of H2S on flowering was abolished in atu2af65a-4 mutants. Transcriptome analyses showed that when AtU2AF65a contained mutations, the regulatory function of H2S during the AS of many flowering genes (including SPA1, LUH, LUG and MAF3) was inhibited. The persulfidation assay showed that AtU2AF65a can be persulfidated by H2S, and the RNA immunoprecipitation data indicated that H2S could alter the binding affinity of AtU2AF65a to the precursor messenger RNA of the above-mentioned flowering genes. Overall, our results suggest that H2S may regulate the AS of flowering-related genes through persulfidation of splicing factor AtU2AF65a and thus lead to early flowering in plants.
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Affiliation(s)
- Tian Ma
- School of Life Science, Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, China
| | - Shutian Xu
- School of Life Science, Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, China
| | - Yaqin Wang
- School of Life Science, Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, China
| | - Liping Zhang
- School of Life Science, Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, China
| | - Zhiqiang Liu
- School of Life Science, Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, China
| | - Danmei Liu
- School of Life Science, Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, China
| | - Zhuping Jin
- School of Life Science, Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, China
| | - Yanxi Pei
- School of Life Science, Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, China
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4
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Larran AS, Pajoro A, Qüesta JI. Is winter coming? Impact of the changing climate on plant responses to cold temperature. PLANT, CELL & ENVIRONMENT 2023; 46:3175-3193. [PMID: 37438895 DOI: 10.1111/pce.14669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/23/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023]
Abstract
Climate change is causing alterations in annual temperature regimes worldwide. Important aspects of this include the reduction of winter chilling temperatures as well as the occurrence of unpredicted frosts, both significantly affecting plant growth and yields. Recent studies advanced the knowledge of the mechanisms underlying cold responses and tolerance in the model plant Arabidopsis thaliana. However, how these cold-responsive pathways will readjust to ongoing seasonal temperature variation caused by global warming remains an open question. In this review, we highlight the plant developmental programmes that depend on cold temperature. We focus on the molecular mechanisms that plants have evolved to adjust their development and stress responses upon exposure to cold. Covering both genetic and epigenetic aspects, we present the latest insights into how alternative splicing, noncoding RNAs and the formation of biomolecular condensates play key roles in the regulation of cold responses. We conclude by commenting on attractive targets to accelerate the breeding of increased cold tolerance, bringing up biotechnological tools that might assist in overcoming current limitations. Our aim is to guide the reflection on the current agricultural challenges imposed by a changing climate and to provide useful information for improving plant resilience to unpredictable cold regimes.
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Affiliation(s)
- Alvaro Santiago Larran
- Centre for Research in Agricultural Genomics (CRAG) IRTA-CSIC-UAB-UB, Campus UAB, Barcelona, Spain
| | - Alice Pajoro
- National Research Council, Institute of Molecular Biology and Pathology, Rome, Italy
| | - Julia I Qüesta
- Centre for Research in Agricultural Genomics (CRAG) IRTA-CSIC-UAB-UB, Campus UAB, Barcelona, Spain
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5
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Kovalchuk I. Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3667. [PMID: 37960024 PMCID: PMC10648063 DOI: 10.3390/plants12213667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023]
Abstract
All species are well adapted to their environment. Stress causes a magnitude of biochemical and molecular responses in plants, leading to physiological or pathological changes. The response to various stresses is genetically predetermined, but is also controlled on the epigenetic level. Most plants are adapted to their environments through generations of exposure to all elements. Many plant species have the capacity to acclimate or adapt to certain stresses using the mechanism of priming. In most cases, priming is a somatic response allowing plants to deal with the same or similar stress more efficiently, with fewer resources diverted from growth and development. Priming likely relies on multiple mechanisms, but the differential expression of non-coding RNAs, changes in DNA methylation, histone modifications, and nucleosome repositioning play a crucial role. Specifically, we emphasize the role of BRM/CHR17, BRU1, FGT1, HFSA2, and H2A.Z proteins as positive regulators, and CAF-1, MOM1, DDM1, and SGS3 as potential negative regulators of somatic stress memory. In this review, we will discuss the role of epigenetic factors in response to stress, priming, and the somatic memory of stress exposures.
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Affiliation(s)
- Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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6
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Rodriguez Gallo MC, Uhrig RG. Phosphorylation mediated regulation of RNA splicing in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1249057. [PMID: 37780493 PMCID: PMC10539000 DOI: 10.3389/fpls.2023.1249057] [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: 06/28/2023] [Accepted: 08/22/2023] [Indexed: 10/03/2023]
Abstract
For the past two decades, the study of alternative splicing (AS) and its involvement in plant development and stress response has grown in popularity. Only recently however, has the focus shifted to the study of how AS regulation (or lack-thereof) affects downstream mRNA and protein landscapes and how these AS regulatory events impact plant development and stress tolerance. In humans, protein phosphorylation represents one of the predominant mechanisms by which AS is regulated and thus the protein kinases governing these phosphorylation events are of interest for further study. Large-scale phosphoproteomic studies in plants have consistently found that RNA splicing-related proteins are extensively phosphorylated, however, the signaling pathways involved in AS regulation have not been resolved. In this mini-review, we summarize our current knowledge of the three major splicing-related protein kinase families in plants that are suggested to mediate AS phospho-regulation and draw comparisons to their metazoan orthologs. We also summarize and contextualize the phosphorylation events identified as occurring on splicing-related protein families to illustrate the high degree to which splicing-related proteins are modified, placing a new focus on elucidating the impacts of AS at the protein and PTM-level.
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Affiliation(s)
| | - R. Glen Uhrig
- University of Alberta, Department of Biological Sciences, Edmonton, AB, Canada
- University of Alberta, Department of Biochemistry, Edmonton, AB, Canada
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7
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Alternative Splicing in the Regulatory Circuit of Plant Temperature Response. Int J Mol Sci 2023; 24:ijms24043878. [PMID: 36835290 PMCID: PMC9962249 DOI: 10.3390/ijms24043878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
As sessile organisms, plants have evolved complex mechanisms to rapidly respond to ever-changing ambient temperatures. Temperature response in plants is modulated by a multilayer regulatory network, including transcriptional and post-transcriptional regulations. Alternative splicing (AS) is an essential post-transcriptional regulatory mechanism. Extensive studies have confirmed its key role in plant temperature response, from adjustment to diurnal and seasonal temperature changes to response to extreme temperatures, which has been well documented by previous reviews. As a key node in the temperature response regulatory network, AS can be modulated by various upstream regulations, such as chromatin modification, transcription rate, RNA binding proteins, RNA structure and RNA modifications. Meanwhile, a number of downstream mechanisms are affected by AS, such as nonsense-mediated mRNA decay (NMD) pathway, translation efficiency and production of different protein variants. In this review, we focus on the links between splicing regulation and other mechanisms in plant temperature response. Recent advances regarding how AS is regulated and the following consequences in gene functional modulation in plant temperature response will be discussed. Substantial evidence suggests that a multilayer regulatory network integrating AS in plant temperature response has been unveiled.
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8
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Ma Z, Li M, Zhang H, Zhao B, Liu Z, Duan S, Meng X, Li G, Guo X. Alternative Splicing of TaHsfA2-7 Is Involved in the Improvement of Thermotolerance in Wheat. Int J Mol Sci 2023; 24:ijms24021014. [PMID: 36674529 PMCID: PMC9861123 DOI: 10.3390/ijms24021014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
High temperature has severely affected plant growth and development, resulting in reduced production of crops worldwide, especially wheat. Alternative splicing (AS), a crucial post-transcriptional regulatory mechanism, is involved in the growth and development of eukaryotes and the adaptation to environmental changes. Previous transcriptome data suggested that heat shock transcription factor (Hsf) TaHsfA2-7 may form different transcripts by AS. However, it remains unclear whether this post-transcriptional regulatory mechanism of TaHsfA2-7 is related to thermotolerance in wheat (Triticum aestivum). Here, we identified a novel splice variant, TaHsfA2-7-AS, which was induced by high temperature and played a positive role in thermotolerance regulation in wheat. Moreover, TaHsfA2-7-AS is predicted to encode a small truncated TaHsfA2-7 isoform, retaining only part of the DNA-binding domain (DBD). TaHsfA2-7-AS is constitutively expressed in various tissues of wheat. Notably, the expression level of TaHsfA2-7-AS is significantly up-regulated by heat shock (HS) during flowering and grain-filling stages in wheat. Further studies showed that TaHsfA2-7-AS was localized in the nucleus but lacked transcriptional activation activity. Ectopic expression of TaHsfA2-7-AS in yeast exhibited improved thermotolerance. Compared to non-transgenic plants, overexpression of TaHsfA2-7-AS in Arabidopsis results in enhanced tolerance to heat stress. Simultaneously, we also found that TaHsfA1 is directly involved in the transcriptional regulation of TaHsfA2-7 and TaHsfA2-7-AS. In summary, our findings demonstrate the function of TaHsfA2-7-AS splicing variant in response to heat stress and establish a link between regulatory mechanisms of AS and the improvement of thermotolerance in wheat.
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Affiliation(s)
- Zhenyu Ma
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Mingyue Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Huaning Zhang
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Baihui Zhao
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Zihui Liu
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Shuonan Duan
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Xiangzhao Meng
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- Correspondence: (X.M.); (G.L.)
| | - Guoliang Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- Correspondence: (X.M.); (G.L.)
| | - Xiulin Guo
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
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9
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Comparative Analysis of Environment-Responsive Alternative Splicing in the Inflorescences of Cultivated and Wild Tomato Species. Int J Mol Sci 2022; 23:ijms231911585. [PMID: 36232886 PMCID: PMC9569760 DOI: 10.3390/ijms231911585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Cultivated tomato (Solanum lycopersicum) is bred for fruit production in optimized environments, in contrast to harsh environments where their ancestral relatives thrive. The process of domestication and breeding has profound impacts on the phenotypic plasticity of plant development and the stress response. Notably, the alternative splicing (AS) of precursor message RNA (pre-mRNA), which is one of the major factors contributing to transcriptome complexity, is responsive to developmental cues and environmental change. To determine a possible association between AS events and phenotypic plasticity, we investigated environment-responsive AS events in the inflorescences of cultivated tomato and its ancestral relatives S. pimpinellifolium. Despite that similar AS frequencies were detected in the cultivated tomato variety Moneymaker and two S. pimpinellifolium accessions under the same growth conditions, 528 genes including splicing factors showed differential splicing in the inflorescences of plants grown in open fields and plastic greenhouses in the Moneymaker variety. In contrast, the two S. pimpinellifolium accessions, LA1589 and LA1781, had 298 and 268 genes showing differential splicing, respectively. Moreover, seven heat responsive genes showed opposite expression patterns in response to changing growth conditions between Moneymaker and its ancestral relatives. Accordingly, there were eight differentially expressed splice variants from genes involved in heat response in Moneymaker. Our results reveal distinctive features of AS events in the inflorescences between cultivated tomato and its ancestral relatives, and show that AS regulation in response to environmental changes is genotype dependent.
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Lee KC, Lee HT, Jeong HH, Park JH, Kim YC, Lee JH, Kim JK. The splicing factor 1-FLOWERING LOCUS M module spatially regulates temperature-dependent flowering by modulating FLOWERING LOCUS T and LEAFY expression. PLANT CELL REPORTS 2022; 41:1603-1612. [PMID: 35589978 DOI: 10.1007/s00299-022-02881-y] [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: 03/05/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
The AtSF1-FLM module spatially controls temperature-dependent flowering by negatively regulating the expression of FT and LFY in the leaf and shoot apex, respectively. Alternative splicing mediated by various splicing factors is important for the regulation of plant growth and development. Our recent reports have shown that a temperature-dependent interaction between Arabidopsis thaliana splicing factor 1 (AtSF1) and FLOWERING LOCUS M (FLM) pre-mRNA introns controls the differential production of FLM-β transcripts at different temperatures, eventually resulting in temperature-responsive flowering. However, the molecular and genetic interactions between the AtSF1-FLM module and floral activator genes remain unknown. Here, we aimed to identify the interactions among AtSF1, FLM, FLOWERING LOCUS T (FT), and LEAFY (LFY) by performing molecular and genetic analyses. FT and TWIN SISTER OF FT (TSF) expression in atsf1-2 mutants significantly increased in the morning and middle of the night at 16 and 23 °C, respectively, under long-day conditions. In addition, ft mutation suppressed the early flowering of atsf1-2 and atsf1-2 flm-3 mutants and masked the temperature response of atsf1-2 flm-3 mutants, suggesting that FT is a downstream target gene of the AtSF1-FLM module. LFY expression significantly increased in the diurnal samples of atsf1-2 mutants and in the shoot apex regions of atsf1-2 ft-10 mutants at different temperatures. The chromatin immunoprecipitation (ChIP) assay revealed that FLM directly binds to the genomic regions of LFY but not of APETALA1 (AP1). Moreover, lfy mutation suppressed the early flowering of flm-3 mutants, suggesting that LFY is another target of the AtSF1-FLM module. Our results reveal that the AtSF1-FLM module spatially modulates temperature-dependent flowering by regulating FT and LFY expressions.
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Affiliation(s)
- Keh Chien Lee
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hee Tae Lee
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hwa Hyun Jeong
- Division of Life Sciences, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, Jeollabuk-do, 54896, Republic of Korea
| | - Jae-Hyeok Park
- Division of Life Sciences, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, Jeollabuk-do, 54896, Republic of Korea
| | - Young-Cheon Kim
- Division of Life Sciences, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, Jeollabuk-do, 54896, Republic of Korea
| | - Jeong Hwan Lee
- Division of Life Sciences, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, Jeollabuk-do, 54896, Republic of Korea.
| | - Jeong-Kook Kim
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
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11
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Tian C, Zhai L, Zhu W, Qi X, Yu Z, Wang H, Chen F, Wang L, Chen S. Characterization of the TCP Gene Family in Chrysanthemum nankingense and the Role of CnTCP4 in Cold Tolerance. PLANTS (BASEL, SWITZERLAND) 2022; 11:936. [PMID: 35406918 PMCID: PMC9002959 DOI: 10.3390/plants11070936] [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: 02/18/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Plant-specific TCP transcription factors play a key role in plant development and stress responses. Chrysanthemum nankingense shows higher cold tolerance than its ornamental polyploid counterpart. However, whether the TCP gene family plays a role in conferring cold tolerance upon C. nankingense remains unknown. Here, we identified 23 CnTCP genes in C. nankingense, systematically analyzed their phylogenetic relationships and synteny with TCPs from other species, and evaluated their expression profiles at low temperature. Phylogenetic analysis of the protein sequences suggested that CnTCP proteins fall into two classes and three clades, with a typical bHLH domain. However, differences between C. nankingense and Arabidopsis in predicted protein structure and binding sites suggested a unique function of CnTCPs in C. nankingense. Furthermore, expression profiles showed that expression of most CnTCPs were downregulated under cold conditions, suggesting their importance in plant responses to cold stress. Notably, expression of miR319 and of its predicted target genes, CnTCP2/4/14, led to fast responses to cold. Overexpression of Arabidopsis CnTCP4 led to hypersensitivity to cold, suggesting that CnTCP4 might play a negative role in C. nankingense responses to cold stress. Our results provide a foundation for future functional genomic studies on this gene family in chrysanthemum.
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Affiliation(s)
- Chang Tian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lisheng Zhai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Wenjing Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Xiangyu Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Zhongyu Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Haibin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Likai Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
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12
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Chang P, Hsieh HY, Tu SL. The U1 snRNP component RBP45d regulates temperature-responsive flowering in Arabidopsis. THE PLANT CELL 2022; 34:834-851. [PMID: 34791475 PMCID: PMC8824692 DOI: 10.1093/plcell/koab273] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/01/2021] [Indexed: 05/26/2023]
Abstract
Precursor messenger RNA (Pre-mRNA) splicing is a crucial step in gene expression whereby the spliceosome produces constitutively and alternatively spliced transcripts. These transcripts not only diversify the transcriptome, but also play essential roles in plant development and responses to environmental changes. Much evidence indicates that regulation at the pre-mRNA splicing step is important for flowering time control; however, the components and detailed mechanism underlying this process remain largely unknown. Here, we identified the splicing factor RNA BINDING PROTEIN 45d (RBP45d), a member of the RBP45/47 family in Arabidopsis thaliana. Using sequence comparison and biochemical analysis, we determined that RBP45d is a component of the U1 small nuclear ribonucleoprotein (U1 snRNP) with functions distinct from other family members. RBP45d associates with the U1 snRNP by interacting with pre-mRNA-processing factor 39a (PRP39a) and directly regulates alternative splicing (AS) for a specific set of genes. Plants with loss of RBP45d and PRP39a function exhibited defects in temperature-induced flowering, potentially due to the misregulation of temperature-sensitive AS of FLOWERING LOCUS M as well as the accumulation of the flowering repressor FLOWERING LOCUS C. Taken together, RBP45d is a U1 snRNP component in plants that functions with PRP39a in temperature-mediated flowering.
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Affiliation(s)
- Ping Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Science, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Hsin-Yu Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Shih-Long Tu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Science, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
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13
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Jian Y, Shim WB, Ma Z. Multiple functions of SWI/SNF chromatin remodeling complex in plant-pathogen interactions. STRESS BIOLOGY 2021; 1:18. [PMID: 37676626 PMCID: PMC10442046 DOI: 10.1007/s44154-021-00019-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/22/2021] [Indexed: 09/08/2023]
Abstract
The SWI/SNF chromatin remodeling complex utilizes the energy of ATP hydrolysis to facilitate chromatin access and plays essential roles in DNA-based events. Studies in animals, plants and fungi have uncovered sophisticated regulatory mechanisms of this complex that govern development and various stress responses. In this review, we summarize the composition of SWI/SNF complex in eukaryotes and discuss multiple functions of the SWI/SNF complex in regulating gene transcription, mRNA splicing, and DNA damage response. Our review further highlights the importance of SWI/SNF complex in regulating plant immunity responses and fungal pathogenesis. Finally, the potentials in exploiting chromatin remodeling for management of crop disease are presented.
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Affiliation(s)
- Yunqing Jian
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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14
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Xie W, Tang Q, Yan F, Tao Z. Transcriptional memory and response to adverse temperatures in plants. J Zhejiang Univ Sci B 2021; 22:791-804. [PMID: 34636184 DOI: 10.1631/jzus.b2100287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Temperature is one of the major environmental signals controlling plant development, geographical distribution, and seasonal behavior. Plants perceive adverse temperatures, such as high, low, and freezing temperatures, as stressful signals that can cause physiological defects and even death. As sessile organisms, plants have evolved sophisticated mechanisms to adapt to recurring stressful environments through changing gene expression or transcriptional reprogramming. Transcriptional memory refers to the ability of primed plants to remember previously experienced stress and acquire enhanced tolerance to similar or different stresses. Epigenetic modifications mediate transcriptional memory and play a key role in adapting to adverse temperatures. Understanding the mechanisms of the formation, maintenance, and resetting of stress-induced transcriptional memory will not only enable us to understand why there is a trade-off between plant defense and growth, but also provide a theoretical basis for generating stress-tolerant crops optimized for future climate change. In this review, we summarize recent advances in dissecting the mechanisms of plant transcriptional memory in response to adverse temperatures, based mainly on studies of the model plant Arabidopsis thaliana. We also discuss remaining questions that are important for further understanding the mechanisms of transcriptional memory during the adverse temperature response.
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Affiliation(s)
- Wei Xie
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China.,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qianqian Tang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China.,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fei Yan
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China.,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zeng Tao
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China. .,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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15
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John S, Olas JJ, Mueller-Roeber B. Regulation of alternative splicing in response to temperature variation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6150-6163. [PMID: 34028544 PMCID: PMC8483784 DOI: 10.1093/jxb/erab232] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/21/2021] [Indexed: 05/08/2023]
Abstract
Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future.
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Affiliation(s)
- Sheeba John
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam, Germany
| | - Justyna Jadwiga Olas
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Correspondence: or
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
- Correspondence: or
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16
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Regional Heritability Mapping of Quantitative Trait Loci Controlling Traits Related to Growth and Productivity in Popcorn (Zea mays L.). PLANTS 2021; 10:plants10091845. [PMID: 34579378 PMCID: PMC8466968 DOI: 10.3390/plants10091845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/17/2022]
Abstract
The method of regional heritability mapping (RHM) has become an important tool in the identification of quantitative trait loci (QTLs) controlling traits of interest in plants. Here, RHM was first applied in a breeding population of popcorn, to identify the QTLs and candidate genes involved in grain yield, plant height, kernel popping expansion, and first ear height, as well as determining the heritability of each significant genomic region. The study population consisted of 98 S1 families derived from the 9th recurrent selection cycle (C-9) of the open-pollinated variety UENF-14, which were genetically evaluated in two environments (ENV1 and ENV2). Seventeen and five genomic regions were mapped by the RHM method in ENV1 and ENV2, respectively. Subsequent genome-wide analysis based on the reference genome B73 revealed associations with forty-six candidate genes within these genomic regions, some of them are considered to be biologically important due to the proteins that they encode. The results obtained by the RHM method have the potential to contribute to knowledge on the genetic architecture of the growth and yield traits of popcorn, which might be used for marker-assisted selection in breeding programs.
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17
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Vitoriano CB, Calixto CPG. Reading between the Lines: RNA-seq Data Mining Reveals the Alternative Message of the Rice Leaf Transcriptome in Response to Heat Stress. PLANTS 2021; 10:plants10081647. [PMID: 34451692 PMCID: PMC8400768 DOI: 10.3390/plants10081647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 11/21/2022]
Abstract
Rice (Oryza sativa L.) is a major food crop but heat stress affects its yield and grain quality. To identify mechanistic solutions to improve rice yield under rising temperatures, molecular responses of thermotolerance must be understood. Transcriptional and post-transcriptional controls are involved in a wide range of plant environmental responses. Alternative splicing (AS), in particular, is a widespread mechanism impacting the stress defence in plants but it has been completely overlooked in rice genome-wide heat stress studies. In this context, we carried out a robust data mining of publicly available RNA-seq datasets to investigate the extension of heat-induced AS in rice leaves. For this, datasets of interest were subjected to filtering and quality control, followed by accurate transcript-specific quantifications. Powerful differential gene expression (DE) and differential AS (DAS) identified 17,143 and 2162 heat response genes, respectively, many of which are novel. Detailed analysis of DAS genes coding for key regulators of gene expression suggests that AS helps shape transcriptome and proteome diversity in response to heat. The knowledge resulting from this study confirmed a widespread transcriptional and post-transcriptional response to heat stress in plants, and it provided novel candidates for rapidly advancing rice breeding in response to climate change.
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18
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Abstract
Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene.
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Affiliation(s)
- Andrzej T Wierzbicki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Todd Blevins
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France;
| | - Szymon Swiezewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland;
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19
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Beyond the Genetic Pathways, Flowering Regulation Complexity in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22115716. [PMID: 34071961 PMCID: PMC8198774 DOI: 10.3390/ijms22115716] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Flowering is one of the most critical developmental transitions in plants’ life. The irreversible change from the vegetative to the reproductive stage is strictly controlled to ensure the progeny’s success. In Arabidopsis thaliana, seven flowering genetic pathways have been described under specific growth conditions. However, the evidence condensed here suggest that these pathways are tightly interconnected in a complex multilevel regulatory network. In this review, we pursue an integrative approach emphasizing the molecular interactions among the flowering regulatory network components. We also consider that the same regulatory network prevents or induces flowering phase change in response to internal cues modulated by environmental signals. In this sense, we describe how during the vegetative phase of development it is essential to prevent the expression of flowering promoting genes until they are required. Then, we mention flowering regulation under suboptimal growing temperatures, such as those in autumn and winter. We next expose the requirement of endogenous signals in flowering, and finally, the acceleration of this transition by long-day photoperiod and temperature rise signals allowing A. thaliana to bloom in spring and summer seasons. With this approach, we aim to provide an initial systemic view to help the reader integrate this complex developmental process.
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20
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Lin J, Zhu Z. Plant responses to high temperature: a view from pre-mRNA alternative splicing. PLANT MOLECULAR BIOLOGY 2021; 105:575-583. [PMID: 33550520 DOI: 10.1007/s11103-021-01117-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/09/2021] [Indexed: 05/14/2023]
Abstract
This review focused on the recent breakthroughs in plant high temperature responses from an alternative splicing angle. With the inevitable global warming, high temperature triggers plants to change their growth and developmental programs for adapting temperature increase. In the past decades, the signaling mechanisms from plant thermo-sensing to downstream transcriptional cascades have been extensively studied. Plenty of elegant review papers have summarized these breakthroughs from signal transduction to cross-talk within plant hormones and environmental cues. Precursor messenger RNA (pre-mRNA) splicing enables plants to produce a series of functional un-related proteins and thus enhances the regulation flexibility. Plants take advantage of this strategy to modulate their proteome diversity under high ambient temperature and elicit developmental plasticity. In this review, we particularly focus on pre-mRNA splicing regulation underlying plant high temperature responses, and will shed new light on the understanding of post-transcriptional regulation on plant growth and development.
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Affiliation(s)
- Jingya Lin
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ziqiang Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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21
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Chang T, Zhao Y, He H, Xi Q, Fu J, Zhao Y. Exogenous melatonin improves growth in hulless barley seedlings under cold stress by influencing the expression rhythms of circadian clock genes. PeerJ 2021; 9:e10740. [PMID: 33552735 PMCID: PMC7831369 DOI: 10.7717/peerj.10740] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/18/2020] [Indexed: 12/01/2022] Open
Abstract
Background Melatonin is a hormone substance that exists in various living organisms. Since it was discovered in the pineal gland of cattle in 1956, the function of melatonin in animals has been roughly clarified. Nevertheless, in plants, the research on melatonin is still insufficient. Hulless barley (Hordeum vulgare L. var. nudum hook. f.) is a crop that originates from cultivated barley in the east, usually grown on the Qinghai-Tibet Plateau, becoming the most important food crop in this area. Although the genome and transcriptome research of highland barley has gradually increased recently years, there are still many problems about how hulless barley adapts to the cold climate of the Qinghai-Tibet Plateau. Methods In this study, we set three temperature conditions 25°C, 15°C, 5°C hulless barley seedlings, and at the same time soaked the hulless barley seeds with a 1 µM melatonin solution for 12 hours before the hulless barley seeds germinated. Afterwards, the growth and physiological indicators of hulless barley seedlings under different treatment conditions were determined. Meanwhile, the qRT-PCR method was used to determine the transcription level of the hulless barley circadian clock genes under different treatment conditions under continuous light conditions. Results The results showed the possible mechanism by which melatonin pretreatment can promote the growth of hulless barley under cold stress conditions by studying the effect of melatonin on the rhythm of the circadian clock system and some physiological indicators. The results revealed that the application of 1 µM melatonin could alleviate the growth inhibition of hulless barley seedlings caused by cold stress. In addition, exogenous melatonin could also restore the circadian rhythmic oscillation of circadian clock genes, such as HvCCA1 and HvTOC1, whose circadian rhythmic phenotypes were lost due to environmental cold stress. Additionally, the results confirmed that exogenous melatonin even reduced the accumulation of key physiological indicators under cold stress, including malondialdehyde and soluble sugars. Discussion Overall, these findings revealed an important mechanism that exogenous melatonin alleviated the inhibition of plant vegetative growths either by restoring the disrupted circadian rhythmic expression oscillations of clock genes, or by regulating the accumulation profiles of pivotal physiological indicators under cold stress.
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Affiliation(s)
- Tianliang Chang
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi'an, China.,Life Sciences School of Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi'an, China
| | - Yi Zhao
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi'an, China.,Life Sciences School of Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi'an, China
| | - Hongyan He
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi'an, China.,Life Sciences School of Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi'an, China
| | - Qianqian Xi
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi'an, China.,Life Sciences School of Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi'an, China
| | - Jiayi Fu
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi'an, China.,Life Sciences School of Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi'an, China
| | - Yuwei Zhao
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi'an, China.,Life Sciences School of Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi'an, China
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22
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Processing of coding and non-coding RNAs in plant development and environmental responses. Essays Biochem 2020; 64:931-945. [DOI: 10.1042/ebc20200029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022]
Abstract
Abstract
Precursor RNAs undergo extensive processing to become mature RNAs. RNA transcripts are subjected to 5′ capping, 3′-end processing, splicing, and modification; they also form dynamic secondary structures during co-transcriptional and post-transcriptional processing. Like coding RNAs, non-coding RNAs (ncRNAs) undergo extensive processing. For example, secondary small interfering RNA (siRNA) transcripts undergo RNA processing, followed by further cleavage to become mature siRNAs. Transcriptome studies have revealed roles for co-transcriptional and post-transcriptional RNA processing in the regulation of gene expression and the coordination of plant development and plant–environment interactions. In this review, we present the latest progress on RNA processing in gene expression and discuss phased siRNAs (phasiRNAs), a kind of germ cell-specific secondary small RNA (sRNA), focusing on their functions in plant development and environmental responses.
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23
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Zhang X, Zhuang L, Liu Y, Yang Z, Huang B. Protein phosphorylation associated with drought priming-enhanced heat tolerance in a temperate grass species. HORTICULTURE RESEARCH 2020; 7:207. [PMID: 33328446 PMCID: PMC7705721 DOI: 10.1038/s41438-020-00440-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is known to play crucial roles in plant tolerance to individual stresses, but how protein phosphorylation is associated with cross-stress tolerance, particularly drought priming-enhanced heat tolerance is largely unknown. The objectives of the present study were to identify phosphorylated proteins and phosphorylation sites that were responsive to drought priming and to determine whether drought priming-enhanced heat tolerance in temperate grass species involves changes in protein phosphorylation. Comparative analysis of phosphoproteomic profiles was performed on leaves of tall fescue (Festuca arundinacea) exposed to heat stress (38/33 °C, day/night) with or without drought priming. A total of 569 differentially regulated phosphoproteins (DRPs) with 1098 phosphorylation sites were identified in response to drought priming or heat stress individually or sequentially. Most DRPs were nuclear-localized and cytosolic proteins. Motif analysis detected [GS], [DSD], and [S..E] as major phosphorylation sites in casein kinase-II and mitogen-activated protein kinases regulated by drought priming and heat stress. Functional annotation and gene ontology analysis demonstrated that DRPs in response to drought priming and in drought-primed plants subsequently exposed to heat stress were mostly enriched in four major biological processes, including RNA splicing, transcription control, stress protection/defense, and stress perception/signaling. These results suggest the involvement of post-translational regulation of the aforementioned biological processes and signaling pathways in drought priming memory and cross-tolerance with heat stress in a temperate grass species.
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Affiliation(s)
- Xiaxiang Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Lili Zhuang
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yu Liu
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhimin Yang
- College of Agro-grassland Science, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Bingru Huang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
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24
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Temperature-Dependent Alternative Splicing of Precursor mRNAs and Its Biological Significance: A Review Focused on Post-Transcriptional Regulation of a Cold Shock Protein Gene in Hibernating Mammals. Int J Mol Sci 2020; 21:ijms21207599. [PMID: 33066638 PMCID: PMC7590145 DOI: 10.3390/ijms21207599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 01/18/2023] Open
Abstract
Multiple mRNA isoforms are often generated during processing such as alternative splicing of precursor mRNAs (pre-mRNA), resulting in a diversity of generated proteins. Alternative splicing is an essential mechanism for the functional complexity of eukaryotes. Temperature, which is involved in all life activities at various levels, is one of regulatory factors for controlling patterns of alternative splicing. Temperature-dependent alternative splicing is associated with various phenotypes such as flowering and circadian clock in plants and sex determination in poikilothermic animals. In some specific situations, temperature-dependent alternative splicing can be evoked even in homothermal animals. For example, the splicing pattern of mRNA for a cold shock protein, cold-inducible RNA-binding protein (CIRP or CIRBP), is changed in response to a marked drop in body temperature during hibernation of hamsters. In this review, we describe the current knowledge about mechanisms and functions of temperature-dependent alternative splicing in plants and animals. Then we discuss the physiological significance of hypothermia-induced alternative splicing of a cold shock protein gene in hibernating and non-hibernating animals.
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25
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Ding Y, Huang L, Jiang Q, Zhu C. MicroRNAs as Important Regulators of Heat Stress Responses in Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11320-11326. [PMID: 32870674 DOI: 10.1021/acs.jafc.0c03597] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Heat stress is a major abiotic stress that significantly affects plant growth and productivity. Plants have, however, evolved complex adaptive mechanisms to cope with heat stress. MicroRNAs (miRNAs) are important molecules that regulate gene expression through the post-transcriptional degradation of target mRNA molecules or by repressing translation. Plant miRNAs play essential roles in development and a variety of stress responses. Recent advances in high-throughput sequencing technologies have enabled the identification and characterization of an increasing number of heat-responsive miRNAs in diverse plant species. Heat-regulated miRNAs combined with their target genes constitute large regulatory networks that control various metabolic pathways, including protein refolding, antioxidant defense, maintenance of photosynthetic systems, protection of reproductive tissues, regulation of flowering time, and miRNA biogenesis. In this review, we summarize the information acquired to date about the significance of plant miRNAs and their target genes in heat stress tolerance, thereby helping to identify the regulatory mechanisms that underlie heat stress responses in plants.
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Affiliation(s)
- Yanfei Ding
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, People's Republic of China
| | - Lingzhi Huang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, People's Republic of China
| | - Qiong Jiang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, People's Republic of China
| | - Cheng Zhu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, People's Republic of China
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Kelly D, Turnbull MH, Jameson PE. Molecular control of masting: an introduction to an epigenetic summer memory. ANNALS OF BOTANY 2020; 125:851-858. [PMID: 31960889 PMCID: PMC7218805 DOI: 10.1093/aob/mcaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 01/09/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Mast flowering ('masting') is characterized by mass synchronized flowering at irregular intervals in populations of perennial plants over a wide geographical area, resulting in irregular high seed production. While masting is a global phenomenon, it is particularly prevalent in the alpine flora of New Zealand. Increases in global temperature may alter the masting pattern, affecting wider communities with a potential impact on plant-pollinator interactions, seed set and food availability for seed-consuming species. SCOPE This review summarizes an ecological temperature model (ΔT) that is being used to predict the intensity of a masting season. We introduce current molecular studies on flowering and the concept of an 'epigenetic summer memory' as a driver of mast flowering. We propose a hypothetical model based on temperature-associated epigenetic modifications of the floral integrator genes FLOWERING LOCUS T, FLOWERING LOCUS C and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1. CONCLUSIONS Genome-wide transcriptomic and targeted gene expression analyses are needed to establish the developmental and physiological processes associated with masting. Such analyses may identify changes in gene expression that can be used to predict the intensity of a forthcoming masting season, as well as to determine the extent to which climate change will influence the mass synchronized flowering of masting species, with downstream impacts on their associated communities.
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Affiliation(s)
- Dave Kelly
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Matthew H Turnbull
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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Kurokawa K, Kobayashi J, Nemoto K, Nozawa A, Sawasaki T, Nakatsuka T, Yamagishi M. Expression of LhFT1, the Flowering Inducer of Asiatic Hybrid Lily, in the Bulb Scales. FRONTIERS IN PLANT SCIENCE 2020; 11:570915. [PMID: 33304361 PMCID: PMC7693649 DOI: 10.3389/fpls.2020.570915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/19/2020] [Indexed: 05/08/2023]
Abstract
Asiatic hybrid lily leaves emerge from their bulbs in spring, after cold exposure in winter, and the plant then blooms in early summer. We identified four FLOWERING LOCUS T (FT)-like genes, LhFT1, LhFT4, LhFT6, and LhFT8, from an Asiatic hybrid lily. Floral bud differentiation initiated within bulbs before the emergence of leaves. LhFT genes were mainly expressed in bulb scales, and hardly in leaves, in which the FT-like genes of many plants are expressed in response to environmental signals. LhFT1 was expressed in bulb scales after vernalization and was correlated to flower bud initiation in two cultivars with different flowering behaviors. LhFT8 was upregulated in bulb scales after cold exposure and three alternative splicing variants with a nonsense codon were simultaneously expressed. LhFT6 was upregulated in bulb scales after flower initiation, whereas LhFT4 was expressed constantly in all organs. LhFT1 overexpression complemented the late-flowering phenotype of Arabidopsis ft-10, whereas that of LhFT8 did so partly. LhFT4 and LhFT6 overexpression could not complement. Yeast two-hybrid and in vitro analyses showed that the LhFT1 protein interacted with the LhFD protein. LhFT6 and LhFT8 proteins also interacted with LhFD, as observed in AlphaScreen assay. Based on these results, we revealed that LhFT1 acts as a floral activator during floral bud initiation in Asiatic hybrid lilies. However, the biological functions of LhFT4, LhFT6, and LhFT8 remain unclear.
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Affiliation(s)
- Kana Kurokawa
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Junya Kobayashi
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | | | - Akira Nozawa
- Proteo-Science Center, Ehime University, Matsuyama, Japan
| | | | - Takashi Nakatsuka
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
- *Correspondence: Takashi Nakatsuka,
| | - Masumi Yamagishi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Lee KC, Chung KS, Lee HT, Park JH, Lee JH, Kim JK. Role of Arabidopsis Splicing factor SF1 in Temperature-Responsive Alternative Splicing of FLM pre-mRNA. FRONTIERS IN PLANT SCIENCE 2020; 11:596354. [PMID: 33335535 PMCID: PMC7735993 DOI: 10.3389/fpls.2020.596354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/11/2020] [Indexed: 05/04/2023]
Abstract
Small changes in temperature affect plant ecological and physiological factors that impact agricultural production. Hence, understanding how temperature affects flowering is crucial for decreasing the effects of climate change on crop yields. Recent reports have shown that FLM-β, the major spliced isoform of FLOWERING LOCUS M (FLM)-a flowering time gene, contributes to temperature-responsive flowering in Arabidopsis thaliana. However, the molecular mechanism linking pre-mRNA processing and temperature-responsive flowering is not well understood. Genetic and molecular analyses identified the role of an Arabidopsis splicing factor SF1 homolog, AtSF1, in regulating temperature-responsive flowering. The loss-of-function AtSF1 mutant shows temperature insensitivity at different temperatures and very low levels of FLM-β transcript, but a significantly increased transcript level of the alternative splicing (AS) isoform, FLM-δ. An RNA immunoprecipitation (RIP) assay revealed that AtSF1 is responsible for ambient temperature-dependent AS of FLM pre-mRNA, resulting in the temperature-dependent production of functional FLM-β transcripts. Moreover, alterations in other splicing factors such as ABA HYPERSENSITIVE1/CBP80 (ABH1/CBP80) and STABILIZED1 (STA1) did not impact the FLM-β/FLM-δ ratio at different temperatures. Taken together, our data suggest that a temperature-dependent interaction between AtSF1 and FLM pre-mRNA controls flowering time in response to temperature fluctuations.
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Affiliation(s)
- Keh Chien Lee
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Kyung Sook Chung
- Division of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Hee Tae Lee
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Jae-Hyeok Park
- Division of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Jeong Hwan Lee
- Division of Life Sciences, Jeonbuk National University, Jeonju, South Korea
- *Correspondence: Jeong-Hwan Lee,
| | - Jeong-Kook Kim
- Division of Life Sciences, Korea University, Seoul, South Korea
- Jeong-Kook Kim,
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The Temperature-Dependent Retention of Introns in GPI8 Transcripts Contributes to a Drooping and Fragile Shoot Phenotype in Rice. Int J Mol Sci 2019; 21:ijms21010299. [PMID: 31906256 PMCID: PMC6982220 DOI: 10.3390/ijms21010299] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/25/2019] [Accepted: 12/30/2019] [Indexed: 12/22/2022] Open
Abstract
Attachment of glycosylphosphatidylinositols (GPIs) to the C-termini of proteins is one of the most common posttranslational modifications in eukaryotic cells. GPI8/PIG-K is the catalytic subunit of the GPI transamidase complex catalyzing the transfer en bloc GPI to proteins. In this study, a T-DNA insertional mutant of rice with temperature-dependent drooping and fragile (df) shoots phenotype was isolated. The insertion site of the T-DNA fragment was 879 bp downstream of the stop codon of the OsGPI8 gene, which caused introns retention in the gene transcripts, especially at higher temperatures. A complementation test confirmed that this change in the OsGPI8 transcripts was responsible for the mutant phenotype. Compared to control plants, internodes of the df mutant showed a thinner shell with a reduced cell number in the transverse direction, and an inhomogeneous secondary wall layer in bundle sheath cells, while many sclerenchyma cells at the tops of the main veins of df leaves were shrunken and their walls were thinner. The df plants also displayed a major reduction in cellulose and lignin content in both culms and leaves. Our data indicate that GPI anchor proteins play important roles in biosynthesis and accumulation of cell wall material, cell shape, and cell division in rice.
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30
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Rapazote-Flores P, Bayer M, Milne L, Mayer CD, Fuller J, Guo W, Hedley PE, Morris J, Halpin C, Kam J, McKim SM, Zwirek M, Casao MC, Barakate A, Schreiber M, Stephen G, Zhang R, Brown JWS, Waugh R, Simpson CG. BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. BMC Genomics 2019; 20:968. [PMID: 31829136 DOI: 10.1186/s12864-019-6243-6247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/29/2019] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants. RESULTS A high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts - BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al. Nature; 544: 427-433, 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al. Plant Physiol; 156: 20-28, 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5' and 3' UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2791 differentially alternatively spliced genes and 2768 transcripts with differential transcript usage. CONCLUSION A high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.
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Affiliation(s)
- Paulo Rapazote-Flores
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Micha Bayer
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Linda Milne
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - John Fuller
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Wenbin Guo
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Pete E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jenny Morris
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Claire Halpin
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Jason Kam
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
- Present address: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Sarah M McKim
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Monika Zwirek
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
- Present Address: MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - M Cristina Casao
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Gordon Stephen
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Runxuan Zhang
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - John W S Brown
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Craig G Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
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31
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Rapazote-Flores P, Bayer M, Milne L, Mayer CD, Fuller J, Guo W, Hedley PE, Morris J, Halpin C, Kam J, McKim SM, Zwirek M, Casao MC, Barakate A, Schreiber M, Stephen G, Zhang R, Brown JWS, Waugh R, Simpson CG. BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. BMC Genomics 2019; 20:968. [PMID: 31829136 PMCID: PMC6907147 DOI: 10.1186/s12864-019-6243-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants. RESULTS A high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts - BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al. Nature; 544: 427-433, 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al. Plant Physiol; 156: 20-28, 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5' and 3' UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2791 differentially alternatively spliced genes and 2768 transcripts with differential transcript usage. CONCLUSION A high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.
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Affiliation(s)
- Paulo Rapazote-Flores
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Micha Bayer
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Linda Milne
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - John Fuller
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Wenbin Guo
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Pete E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jenny Morris
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Claire Halpin
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Jason Kam
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
- Present address: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Sarah M McKim
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Monika Zwirek
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
- Present Address: MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - M Cristina Casao
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Gordon Stephen
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Runxuan Zhang
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - John W S Brown
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Craig G Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
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Rigo R, Bazin JRM, Crespi M, Charon CL. Alternative Splicing in the Regulation of Plant-Microbe Interactions. PLANT & CELL PHYSIOLOGY 2019; 60:1906-1916. [PMID: 31106828 DOI: 10.1093/pcp/pcz086] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/22/2019] [Indexed: 05/16/2023]
Abstract
As sessile organisms, plants are continuously exposed to a wide range of biotic interactions. While some biotic interactions are beneficial or even essential for the plant (e.g. rhizobia and mycorrhiza), others such as pathogens are detrimental and require fast adaptation. Plants partially achieve this growth and developmental plasticity by modulating the repertoire of genes they express. In the past few years, high-throughput transcriptome sequencing have revealed that, in addition to transcriptional control of gene expression, post-transcriptional processes, notably alternative splicing (AS), emerged as a key mechanism for gene regulation during plant adaptation to the environment. AS not only can increase proteome diversity by generating multiple transcripts from a single gene but also can reduce gene expression by yielding isoforms degraded by mechanisms such as nonsense-mediated mRNA decay. In this review, we will summarize recent discoveries detailing the contribution of AS to the regulation of plant-microbe interactions, with an emphasis on the modulation of immunity receptor function and other components of the signaling pathways that deal with pathogen responses. We will also discuss emerging evidences that AS could contribute to dynamic reprogramming of the plant transcriptome during beneficial interactions, such as the legume-symbiotic interaction.
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Affiliation(s)
- Richard Rigo
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Universite Paris-Saclay, Orsay Cedex, France
| | - Jï Rï Mie Bazin
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Universite Paris-Saclay, Orsay Cedex, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Universite Paris-Saclay, Orsay Cedex, France
| | - Cï Line Charon
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Universite Paris-Saclay, Orsay Cedex, France
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33
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Healy TM, Schulte PM. Patterns of alternative splicing in response to cold acclimation in fish. ACTA ACUST UNITED AC 2019; 222:jeb.193516. [PMID: 30692167 DOI: 10.1242/jeb.193516] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/23/2019] [Indexed: 12/26/2022]
Abstract
Phenotypic plasticity is an important aspect of an organism's response to environmental change that often requires the modulation of gene expression. These changes in gene expression can be quantitative, as a result of increases or decreases in the amounts of specific transcripts, or qualitative, as a result of the expression of alternative transcripts from the same gene (e.g. via alternative splicing of pre-mRNAs). Although the role of quantitative changes in gene expression in phenotypic plasticity is well known, relatively few studies have examined the role of qualitative changes. Here, we use skeletal muscle RNA-seq data from Atlantic killifish (Fundulus heteroclitus), threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio) to investigate the extent of qualitative changes in gene expression in response to cold acclimation. Fewer genes demonstrated alternative splicing than differential expression as a result of cold acclimation; however, differences in splicing were detected for 426 to 866 genes depending on species, indicating that large numbers of qualitative changes in gene expression are associated with cold acclimation. Many of these alternatively spliced genes were also differentially expressed, and there was functional enrichment for involvement in muscle contraction among the genes demonstrating qualitative changes in response to cold acclimation. Additionally, there was a common group of 29 genes with cold-acclimation-mediated changes in splicing in all three species, suggesting that there may be a set of genes with expression patterns that respond qualitatively to prolonged exposure to cold temperatures across fishes.
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Affiliation(s)
- Timothy M Healy
- The University of British Columbia, Department of Zoology, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
| | - Patricia M Schulte
- The University of British Columbia, Department of Zoology, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
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34
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Abstract
Assembly of the barley genome and extensive use of RNA-seq has resulted in an abundance of gene expression data and the recognition of wide-scale production of alternatively spliced transcripts. Here, we describe in detail a high-resolution reverse transcription-PCR based panel (HR RT-PCR) that confirms the accuracy of alternatively spliced transcripts from RNA-seq and allows quantification of changes in the proportion of splice isoforms between different experimental conditions, time points, tissues, genotypes, ecotypes, and treatments. By validating a selection of barley genes, use of the panel gives confidence or otherwise to the genome-wide global changes in alternatively spliced transcripts reported by RNA-seq. This simple assay can readily be applied to perform detailed transcript isoform analysis for any gene in any species.
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35
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Nibau C, Gallemí M, Dadarou D, Doonan JH, Cavallari N. Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2. FRONTIERS IN PLANT SCIENCE 2019; 10:1680. [PMID: 32038671 PMCID: PMC6987439 DOI: 10.3389/fpls.2019.01680] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/29/2019] [Indexed: 05/05/2023]
Abstract
The ability to sense environmental temperature and to coordinate growth and development accordingly, is critical to the reproductive success of plants. Flowering time is regulated at the level of gene expression by a complex network of factors that integrate environmental and developmental cues. One of the main players, involved in modulating flowering time in response to changes in ambient temperature is FLOWERING LOCUS M (FLM). FLM transcripts can undergo extensive alternative splicing producing multiple variants, of which FLM-β and FLM-δ are the most representative. While FLM-β codes for the flowering repressor FLM protein, translation of FLM-δ has the opposite effect on flowering. Here we show that the cyclin-dependent kinase G2 (CDKG2), together with its cognate cyclin, CYCLYN L1 (CYCL1) affects the alternative splicing of FLM, balancing the levels of FLM-β and FLM-δ across the ambient temperature range. In the absence of the CDKG2/CYCL1 complex, FLM-β expression is reduced while FLM-δ is increased in a temperature dependent manner and these changes are associated with an early flowering phenotype in the cdkg2 mutant lines. In addition, we found that transcript variants retaining the full FLM intron 1 are sequestered in the cell nucleus. Strikingly, FLM intron 1 splicing is also regulated by CDKG2/CYCL1. Our results provide evidence that temperature and CDKs regulate the alternative splicing of FLM, contributing to flowering time definition.
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Affiliation(s)
- Candida Nibau
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- *Correspondence: Nicola Cavallari, ; Candida Nibau,
| | - Marçal Gallemí
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Despoina Dadarou
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - John H. Doonan
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Nicola Cavallari
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna, Austria
- *Correspondence: Nicola Cavallari, ; Candida Nibau,
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36
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Leijten W, Koes R, Roobeek I, Frugis G. Translating Flowering Time From Arabidopsis thaliana to Brassicaceae and Asteraceae Crop Species. PLANTS 2018; 7:plants7040111. [PMID: 30558374 PMCID: PMC6313873 DOI: 10.3390/plants7040111] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/07/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022]
Abstract
Flowering and seed set are essential for plant species to survive, hence plants need to adapt to highly variable environments to flower in the most favorable conditions. Endogenous cues such as plant age and hormones coordinate with the environmental cues like temperature and day length to determine optimal time for the transition from vegetative to reproductive growth. In a breeding context, controlling flowering time would help to speed up the production of new hybrids and produce high yield throughout the year. The flowering time genetic network is extensively studied in the plant model species Arabidopsis thaliana, however this knowledge is still limited in most crops. This article reviews evidence of conservation and divergence of flowering time regulation in A. thaliana with its related crop species in the Brassicaceae and with more distant vegetable crops within the Asteraceae family. Despite the overall conservation of most flowering time pathways in these families, many genes controlling this trait remain elusive, and the function of most Arabidopsis homologs in these crops are yet to be determined. However, the knowledge gathered so far in both model and crop species can be already exploited in vegetable crop breeding for flowering time control.
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Affiliation(s)
- Willeke Leijten
- ENZA Zaden Research & Development B.V., Haling 1E, 1602 DB Enkhuizen, The Netherlands.
| | - Ronald Koes
- Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Ilja Roobeek
- ENZA Zaden Research & Development B.V., Haling 1E, 1602 DB Enkhuizen, The Netherlands.
| | - Giovanna Frugis
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300 ⁻ 00015, Monterotondo Scalo, Roma, Italy.
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37
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Capovilla G, Delhomme N, Collani S, Shutava I, Bezrukov I, Symeonidi E, de Francisco Amorim M, Laubinger S, Schmid M. PORCUPINE regulates development in response to temperature through alternative splicing. NATURE PLANTS 2018; 4:534-539. [PMID: 29988152 DOI: 10.1038/s41477-018-0176-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/14/2018] [Indexed: 05/20/2023]
Abstract
Recent findings suggest that alternative splicing has a critical role in controlling the responses of plants to temperature variations. However, alternative splicing factors in plants are largely uncharacterized. Here we establish the putative splice regulator, PORCUPINE (PCP), as temperature-specific regulator of development in Arabidopsis thaliana. Our findings point to the misregulation of WUSCHEL and CLAVATA3 as the possible cause for the meristem defects affecting the pcp-1 loss-of-function mutants at low temperatures.
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Affiliation(s)
- Giovanna Capovilla
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany
| | - Nicolas Delhomme
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University for Agricultural Sciences, Umeå, Sweden
| | - Silvio Collani
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Iryna Shutava
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Ilja Bezrukov
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany
| | - Efthymia Symeonidi
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany
| | | | - Sascha Laubinger
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
- Institute for Biology and Environmental Sciences (IBU), University of Oldenburg, Oldenburg, Germany
| | - Markus Schmid
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany.
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden.
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38
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Severing E, Faino L, Jamge S, Busscher M, Kuijer-Zhang Y, Bellinazzo F, Busscher-Lange J, Fernández V, Angenent GC, Immink RGH, Pajoro A. Arabidopsis thaliana ambient temperature responsive lncRNAs. BMC PLANT BIOLOGY 2018; 18:145. [PMID: 30005624 PMCID: PMC6045843 DOI: 10.1186/s12870-018-1362-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/04/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have emerged as new class of regulatory molecules in animals where they regulate gene expression at transcriptional and post-transcriptional level. Recent studies also identified lncRNAs in plant genomes, revealing a new level of transcriptional complexity in plants. Thousands of lncRNAs have been predicted in the Arabidopsis thaliana genome, but only a few have been studied in depth. RESULTS Here we report the identification of Arabidopsis lncRNAs that are expressed during the vegetative stage of development in either the shoot apical meristem or in leaves. We found that hundreds of lncRNAs are expressed in these tissues, of which 50 show differential expression upon an increase in ambient temperature. One of these lncRNAs, FLINC, is down-regulated at higher ambient temperature and affects ambient temperature-mediated flowering in Arabidopsis. CONCLUSION A number of ambient temperature responsive lncRNAs were identified with potential roles in the regulation of temperature-dependent developmental changes, such as the transition from the vegetative to the reproductive (flowering) phase. The challenge for the future is to characterize the biological function and molecular mode of action of the large number of ambient temperature-regulated lncRNAs that have been identified in this study.
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Affiliation(s)
- Edouard Severing
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Suraj Jamge
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Marco Busscher
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Yang Kuijer-Zhang
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Francesca Bellinazzo
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | | | | | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Richard G. H. Immink
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Alice Pajoro
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
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39
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Liu W, Lin Z, Liu Y, Lin Y, Xu X, Lai Z. Genome-wide identification and characterization of the CKII gene family in the cultivated banana cultivar (Musa spp. cv Tianbaojiao) and the wild banana (Musa itinerans). PLoS One 2018; 13:e0200149. [PMID: 29995937 PMCID: PMC6040749 DOI: 10.1371/journal.pone.0200149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/20/2018] [Indexed: 11/19/2022] Open
Abstract
Plant casein kinase II (CKII) plays an essential role in regulating plant growth and development, and responses to biotic and abiotic stresses. Here, we report the identification and characterization of the CKII family genes in Musa spp. cv. ‘Tianbaojiao’ (AAA group) and the wild banana (Musa itinerans). The 13 cDNA sequences of the CKII family members were identified both in ‘Tianbaojiao’ and wild banana, respectively. The differences between CKII α and CKII β members are corroborated through the subcellular localizations, phosphorylation sites and gene structures. The cloning of CKII β-like-2 gDNA sequences in wild banana and ‘Tianbaojiao’ and the analysis of gene structures showed MiCKIIβ-like-2b and MaCKIIβ-like-2 are likely alternatively spliced transcripts, which were derived from the alternative splicing events that involved exon deletion. The qPCR validation showed differential expression CKII family members in response to cold stress and also in all tested tissues (leaf, pseudostem and root) of wild banana. In particular, the normal transcript MiCKIIβ-like-2a was highly expressed in response to cold stress in wild banana; oppositely, the alternatively spliced transcript MiCKIIβ-like-2b was quite lowly expressed. The complex origin and long-term evolution of Musa lineage might explain the alternative splicing events of CKII β-like-2.
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Affiliation(s)
- Weihua Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhengchun Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yanying Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - XuHan Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- * E-mail:
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40
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James AB, Sullivan S, Nimmo HG. Global spatial analysis of Arabidopsis natural variants implicates 5'UTR splicing of LATE ELONGATED HYPOCOTYL in responses to temperature. PLANT, CELL & ENVIRONMENT 2018; 41. [PMID: 29520807 PMCID: PMC6033021 DOI: 10.1111/pce.13188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
How plants perceive and respond to temperature remains an important question in the plant sciences. Temperature perception and signal transduction may occur through temperature-sensitive intramolecular folding of primary mRNA transcripts. Recent studies suggested a role for retention of the first intron in the 5'UTR of the clock component LATE ELONGATED HYPOCOTYL (LHY) in response to changes in temperature. Here, we identified a set of haplotypes in the LHY 5'UTR, examined their global spatial distribution, and obtained evidence that haplotype can affect temperature-dependent splicing of LHY transcripts. Correlations of haplotype spatial distributions with global bioclimatic variables and altitude point to associations with annual mean temperature and temperature fluctuation. Relatively rare relict type accessions correlate with lower mean temperature and greater temperature fluctuation and the spatial distribution of other haplotypes may be informative of evolutionary processes driving colonization of ecosystems. We propose that haplotypes may possess distinct 5'UTR pre-mRNA folding thermodynamics and/or specific biological stabilities based around the binding of trans-acting RNA splicing factors, a consequence of which is scalable splicing sensitivity of a central clock component that is likely tuned to specific temperature environments.
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Affiliation(s)
- Allan B. James
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Stuart Sullivan
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Hugh G. Nimmo
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
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41
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Dixon LE, Farré A, Finnegan EJ, Orford S, Griffiths S, Boden SA. Developmental responses of bread wheat to changes in ambient temperature following deletion of a locus that includes FLOWERING LOCUS T1. PLANT, CELL & ENVIRONMENT 2018; 41:1715-1725. [PMID: 29314053 PMCID: PMC6033019 DOI: 10.1111/pce.13130] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/16/2017] [Accepted: 11/26/2017] [Indexed: 05/18/2023]
Abstract
FLOWERING LOCUS T (FT) is a central integrator of environmental signals that regulates the timing of vegetative to reproductive transition in flowering plants. In model plants, these environmental signals have been shown to include photoperiod, vernalization, and ambient temperature pathways, and in crop species, the integration of the ambient temperature pathway remains less well understood. In hexaploid wheat, at least 5 FT-like genes have been identified, each with a copy on the A, B, and D genomes. Here, we report the characterization of FT-B1 through analysis of FT-B1 null and overexpression genotypes under different ambient temperature conditions. This analysis has identified that the FT-B1 alleles perform differently under diverse environmental conditions; most notably, the FT-B1 null produces an increase in spikelet and tiller number when grown at lower temperature conditions. Additionally, absence of FT-B1 facilitates more rapid germination under both light and dark conditions. These results provide an opportunity to understand the FT-dependent pathways that underpin key responses of wheat development to changes in ambient temperature. This is particularly important for wheat, for which development and grain productivity are sensitive to changes in temperature.
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Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan JH. The cyclin-dependent kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:1010-1022. [PMID: 29602264 PMCID: PMC6032924 DOI: 10.1111/tpj.13914] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/15/2018] [Accepted: 03/13/2018] [Indexed: 05/19/2023]
Abstract
The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the cyclin-dependent kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the cyclin-dependent kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 (CYCL1), resulting in two distinct messenger RNAs. The relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing (AS) of CDKG1 and regulated by CDKG2 and CYCL1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts, and this in turn translates into differential CDKG1 protein expression coordinating the AS of ATU2AF65A.
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Affiliation(s)
- Nicola Cavallari
- Max F. Perutz LaboratoriesMedical University of ViennaVienna Biocenter, Dr Bohr‐Gasse 9/3A‐1030WienAustria
- Present address:
Institute of Science and Technology AustriaAm Campus 13400KlosterneuburgAustria
| | - Candida Nibau
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythSY23 3EBUK
| | - Armin Fuchs
- Max F. Perutz LaboratoriesMedical University of ViennaVienna Biocenter, Dr Bohr‐Gasse 9/3A‐1030WienAustria
| | - Despoina Dadarou
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythSY23 3EBUK
| | - Andrea Barta
- Max F. Perutz LaboratoriesMedical University of ViennaVienna Biocenter, Dr Bohr‐Gasse 9/3A‐1030WienAustria
| | - John H. Doonan
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythSY23 3EBUK
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Effects of cold acclimation and dsRNA injections on Gs1l gene splicing in Drosophila montana. Sci Rep 2018; 8:7577. [PMID: 29765071 PMCID: PMC5953924 DOI: 10.1038/s41598-018-25872-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 04/26/2018] [Indexed: 01/27/2023] Open
Abstract
Alternative splicing, in which one gene produce multiple transcripts, may influence how adaptive genes respond to specific environments. A newly produced transcriptome of Drosophila montana shows the Gs1-like (Gs1l) gene to express multiple splice variants and to be down regulated in cold acclimated flies with increased cold tolerance. Gs1l’s effect on cold tolerance was further tested by injecting cold acclimated and non-acclimated flies from two distantly located northern and southern fly populations with double stranded RNA (dsRNA) targeting Gs1l. While both populations had similar cold acclimation responses, dsRNA injections only effected the northern population. The nature of splicing expression was then investigated in the northern population by confirming which Gs1l variants are present, by comparing the expression of different gene regions and by predicting the protein structures of splices using homology modelling. We find different splices of Gs1l not only appear to have independent impacts on cold acclimation but also elicit different effects in populations originating from two very different environments. Also, at the protein level, Gs1l appears homologous to the human HDHD1A protein and some splices might produce functionally different proteins though this needs to be verified in future studies by measuring the particular protein levels. Taken together, Gs1l appears to be an interesting new candidate to test how splicing influences adaptations.
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44
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Genome-wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley. Sci Rep 2018; 8:7085. [PMID: 29728569 PMCID: PMC5935748 DOI: 10.1038/s41598-018-25349-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/11/2018] [Indexed: 12/20/2022] Open
Abstract
The SQUAMOSA-promoter binding like (SPL) gene family encodes transcription factors that have been shown in many species to influence plant growth and development, but information about these genes in barley (Hordeum vulgare L.) is limited. This study identified 17 barley SPL genes, within eight distinct groups, that are orthologs of SPL genes described in Arabidopsis, wheat, and rice. Sixteen barley SPLs undergo alternative splicing. Seven SPLs contain a putative miR156 target site and the transcript levels of the miR156-targeted HvSPLs (HvSPL3, 13 and 23) were lower in vegetative than in reproductive phase but this was true also for some SPL genes such as HvSPL6 that were not regulated by miR156. Because SPL gene products regulate miR172, which is also involved in floral development, the expression of miR172 was studied. An antagonistic expression pattern of miR156 and miR172b during the vegetative and the reproductive phases signifies their apparent function in barley growth phase transition. Characterization of a barley mir172 mutant having an abnormal, indeterminate spikelet phenotype suggests the possible feedback role of AP2/miR172 module on HvSPL genes. This is the first comprehensive analysis of the miR156/SPL/miR172 axis in barley that provides a basis to elucidate their roles in various biological processes.
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45
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Jung I, Kang H, Kim JU, Chang H, Kim S, Jung W. The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature. BMC SYSTEMS BIOLOGY 2018; 12:27. [PMID: 29560829 PMCID: PMC5861484 DOI: 10.1186/s12918-018-0548-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Panax ginseng C.A.Meyer) in Korea have migrated from mid to northern parts of the Korean peninsula to escape from the various higher temperature related stresses. Under the high ambient temperature, vegetative growth was accelerated, which resulted in early flowering. This precocious phase change led to yield loss. Despite of its importance as a traditional medicine, biological mechanisms of ginseng has not been well studied and even the genome sequence of ginseng is yet to be determined due to its complex genome structure. Thus, it is challenging to investigate the molecular biology mechanisms at the transcript level. RESULTS To investigate how ginseng responds to the high ambient temperature environment, we performed high throughput RNA sequencing and implemented a bioinformatics pipeline for the integrated analysis of small-RNA and mRNA-seq data without a reference genome. By performing reverse transcriptase (RT) PCR and sanger sequencing of transcripts that were assembled using our pipeline, we validated that their sequences were expressed in our samples. Furthermore, to investigate the interaction between genes and non-coding small RNAs and their regulation status under the high ambient temperature, we identified potential gene regulatory miRNAs. As a result, 100,672 contigs with significant expression level were identified and 6 known, 214 conserved and 60 potential novel miRNAs were predicted to be expressed under the high ambient temperature. CONCLUSION Collectively, we have found that development, flowering and temperature responsive genes were induced under high ambient temperature, whereas photosynthesis related genes were repressed. Functional miRNAs were down-regulated under the high ambient temperature. Among them are miR156 and miR396 that target flowering (SPL6/9) and growth regulating genes (GRF) respectively.
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Affiliation(s)
- Inuk Jung
- Bioinformatics Institute, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea
| | - Hyejin Kang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea
| | - Jang Uk Kim
- National Institute of Horticultural and Herbal Science, Ginseng Research Division, RDA, Eumsung-gun, Chungbuk, Republic of Korea
| | - Hyeonsook Chang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea
| | - Sun Kim
- Bioinformatics Institute, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea.,Department of Computer Science and Engineering, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea
| | - Woosuk Jung
- Department of Applied Bioscience, Konkuk University, Gwangjin-Gu, Seoul, Republic of Korea.
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Lee SS, Jung WY, Park HJ, Lee A, Kwon SY, Kim HS, Cho HS. Genome-wide Analysis of Alternative Splicing in An Inbred Cabbage ( Brassica oleracea L.) Line 'HO' in Response to Heat Stress. Curr Genomics 2017; 19:12-20. [PMID: 29491729 PMCID: PMC5817872 DOI: 10.2174/1389202918666170705151901] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 11/01/2016] [Accepted: 11/15/2016] [Indexed: 11/29/2022] Open
Abstract
Introduction: High-throughput RNA sequencing (RNA-Seq) studies demonstrate that Alter-native Splicing (AS) is a widespread mechanism that enhances transcriptome diversity, particularly in plants exposed to environmental stress. In an attempt to determine the transcriptome and AS patterns of cabbage inbred line “HO” under Heat Stress (HS), RNA-Seq was carried out using HS-treated and con-trol samples. Genome-wide analysis indicated that AS is differentially regulated in response to HS. The number of AS events markedly increased in HS-treated samples compared to the control. Conclusion: We identified 1,864 genes, including Heat shock transcription factor (Hsf) and heat shock protein (Hsp) genes, that exhibited >4-fold changes in expression upon exposure to HS. The enriched Gene Ontology (GO) terms of the 1,864 genes included ‘response to stress/abiotic stimulus/chemical stimulus’, among, which the genes most highly induced by HS encode small Hsps and Hsf proteins. The heat-induced genes also showed an increased number of AS events under HS conditions. In addi-tion, the distribution of AS types was altered under HS conditions, as the level of Intron Retention (IR) decreased, whereas other types of AS increased, under these conditions. Severe HS-induced AS was al-so observed in Hsfs and Hsps, which play crucial roles in regulating heat tolerance. Our results support the notion that AS of HS-related genes, such as HsfA2 and HsfB2a, are important for heat stress adapta-tion in cabbage.
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Affiliation(s)
- Sang Sook Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Won Yong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Arum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.,Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.,Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34113, Korea
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Abstract
This article comments on: Capovilla G, Symeonidi E, Wu R, Schmid M. 2017. Contribution of major FLM isoforms to temperature-dependent mediated flowering in Arabidopsis thaliana. Journal of Experimental Botany 68, 5117–5127.
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Affiliation(s)
- Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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48
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Liu Q, Yan S, Yang T, Zhang S, Chen YQ, Liu B. Small RNAs in regulating temperature stress response in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:774-791. [PMID: 28731217 DOI: 10.1111/jipb.12571] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/12/2017] [Indexed: 05/21/2023]
Abstract
Due to global climate change, temperature stress has become one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms in plants, particularly in the identification of temperature stress responsive protein-coding genes. Recently discovered microRNAs (miRNAs) and endogenous small-interfering RNAs (siRN As) have also been demonstrated as important players in plant temperature stress response. Using high-throughput sequencing, many small RNAs, especially miRNAs, have been identified to be triggered by cold or heat. Subsequently, several studies have shown an important functional role for these small RNAs in cold or heat tolerance. These findings greatly broaden our understanding of endogenous small RNAs in plant stress response control. Here, we highlight new findings regarding the roles of miRNAs and siRNAs in plant temperature stress response and acclimation. We also review the current understanding of the regulatory mechanisms of small RNAs in temperature stress response, and explore the outlook for the use of these small RNAs in molecular breeding for improvement of temperature stress tolerance in plants.
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Affiliation(s)
- Qing Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Tifeng Yang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shaohong Zhang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yue-Qin Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Bin Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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Haak DC, Fukao T, Grene R, Hua Z, Ivanov R, Perrella G, Li S. Multilevel Regulation of Abiotic Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1564. [PMID: 29033955 PMCID: PMC5627039 DOI: 10.3389/fpls.2017.01564] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/28/2017] [Indexed: 05/18/2023]
Abstract
The sessile lifestyle of plants requires them to cope with stresses in situ. Plants overcome abiotic stresses by altering structure/morphology, and in some extreme conditions, by compressing the life cycle to survive the stresses in the form of seeds. Genetic and molecular studies have uncovered complex regulatory processes that coordinate stress adaptation and tolerance in plants, which are integrated at various levels. Investigating natural variation in stress responses has provided important insights into the evolutionary processes that shape the integrated regulation of adaptation and tolerance. This review primarily focuses on the current understanding of how transcriptional, post-transcriptional, post-translational, and epigenetic processes along with genetic variation orchestrate stress responses in plants. We also discuss the current and future development of computational tools to identify biologically meaningful factors from high dimensional, genome-scale data and construct the signaling networks consisting of these components.
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Affiliation(s)
- David C. Haak
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, BlacksburgVA, United States
| | - Takeshi Fukao
- Department of Crop and Soil Environmental Sciences, Virginia Tech, BlacksburgVA, United States
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, BlacksburgVA, United States
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, AthensOH, United States
| | - Rumen Ivanov
- Institut für Botanik, Heinrich-Heine-Universität DüsseldorfDüsseldorf, Germany
| | - Giorgio Perrella
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, United Kingdom
| | - Song Li
- Department of Crop and Soil Environmental Sciences, Virginia Tech, BlacksburgVA, United States
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50
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Zhang XH, Lian XD, Dai ZX, Zheng HY, Chen X, Zheng YT. α3-Deletion Isoform of HLA-A11 Modulates Cytotoxicity of NK Cells: Correlations with HIV-1 Infection of Cells. THE JOURNAL OF IMMUNOLOGY 2017; 199:2030-2042. [PMID: 28784847 DOI: 10.4049/jimmunol.1602183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 07/14/2017] [Indexed: 01/16/2023]
Abstract
Alternative splicing occurs frequently in many genes, especially those involved in immunity. Unfortunately, the functions of many alternatively spliced molecules from immunologically relevant genes remain unknown. Classical HLA-I molecules are expressed on almost all nucleated cells and play a pivotal role in both innate and adaptive immunity. Although splice variants of HLA-I genes have been reported, the details of their functions have not been reported. In the current study, we determined the characteristics, expression, and function of a novel splice variant of HLA-A11 named HLA-A11svE4 HLA-A11svE4 is located on the cell surface without β2-microglobulin (β2m). Additionally, HLA-A11svE4 forms homodimers as well as heterodimers with HLA-A open conformers, instead of combining with β2m. Moreover, HLA-A11svE4 inhibits the activation of NK cells to protect target cells. Compared with β2m and HLA-A11, the heterodimer of HLA-A11svE4 and HLA-A11 protected target cells from lysis by NK cells more effectively. Furthermore, HLA-AsvE4 expression was upregulated by HIV-1 in vivo and by HSV, CMV, and hepatitis B virus in vitro. In addition, our findings indicated that HLA-A11svE4 molecules were functional in activating CD8+ T cells through Ag presentation. Taken together, these results suggested that HLA-A11svE4 can homodimerize and form a novel heterodimeric complex with HLA-A11 open conformers. Furthermore, the data are consistent with HLA-A11svE4 playing a role in the immune escape of HIV-1.
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Affiliation(s)
- Xi-He Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; and
| | - Xiao-Dong Lian
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; and
| | - Zheng-Xi Dai
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hong-Yi Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; and
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
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